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Al Shihabi A, Tebon PJ, Nguyen HTL, Chantharasamee J, Sartini S, Davarifar A, Jensen AY, Diaz-Infante M, Cox H, Gonzalez AE, Norris S, Sperry J, Nakashima J, Tavanaie N, Winata H, Fitz-Gibbon ST, Yamaguchi TN, Jeong JH, Dry S, Singh AS, Chmielowski B, Crompton JG, Kalbasi AK, Eilber FC, Hornicek F, Bernthal NM, Nelson SD, Boutros PC, Federman NC, Yanagawa J, Soragni A. The landscape of drug sensitivity and resistance in sarcoma. Cell Stem Cell 2024:S1934-5909(24)00296-0. [PMID: 39305899 DOI: 10.1016/j.stem.2024.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 06/14/2024] [Accepted: 08/21/2024] [Indexed: 09/25/2024]
Abstract
Sarcomas are rare malignancies with over 100 distinct histological subtypes. Their rarity and heterogeneity pose significant challenges to identifying effective therapies, and approved regimens show varied responses. Novel, personalized approaches to therapy are needed to improve patient outcomes. Patient-derived tumor organoids (PDTOs) model tumor behavior across an array of malignancies. We leverage PDTOs to characterize the landscape of drug resistance and sensitivity in sarcoma, collecting 194 specimens from 126 patients spanning 24 distinct sarcoma subtypes. Our high-throughput organoid screening pipeline tested single agents and combinations, with results available within a week from surgery. Drug sensitivity correlated with clinical features such as tumor subtype, treatment history, and disease trajectory. PDTO screening can facilitate optimal drug selection and mirror patient outcomes in sarcoma. We could identify at least one FDA-approved or NCCN-recommended effective regimen for 59% of the specimens, demonstrating the potential of our pipeline to provide actionable treatment information.
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Affiliation(s)
- Ahmad Al Shihabi
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peyton J Tebon
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Huyen Thi Lam Nguyen
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jomjit Chantharasamee
- Division of Hematology-Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sara Sartini
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ardalan Davarifar
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Division of Hematology-Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexandra Y Jensen
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Miranda Diaz-Infante
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hannah Cox
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Summer Norris
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Nasrin Tavanaie
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Helena Winata
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sorel T Fitz-Gibbon
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jae H Jeong
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarah Dry
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Arun S Singh
- Division of Hematology-Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bartosz Chmielowski
- Division of Hematology-Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joseph G Crompton
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Division of Surgical Oncology David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anusha K Kalbasi
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Fritz C Eilber
- Division of Surgical Oncology David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Francis Hornicek
- Department of Orthopedic Surgery, University of Miami, Miami, FL, USA
| | - Nicholas M Bernthal
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Scott D Nelson
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Noah C Federman
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jane Yanagawa
- Department of Surgery, Division of Thoracic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alice Soragni
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA.
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2
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Martín R, Gaitán N, Jarlier F, Feuerbach L, de Soyres H, Arbonés M, Gutman T, Puiggròs M, Ferriz A, Gonzalez A, Estelles L, Gut I, Capella-Gutierrez S, Stein LD, Brors B, Royo R, Hupé P, Torrents D. ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers. CELL GENOMICS 2024; 4:100639. [PMID: 39216474 DOI: 10.1016/j.xgen.2024.100639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/13/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.
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Affiliation(s)
- Rodrigo Martín
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Nicolás Gaitán
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Frédéric Jarlier
- Institut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France
| | - Lars Feuerbach
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Henri de Soyres
- Institut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France
| | - Marc Arbonés
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Tom Gutman
- Institut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France
| | - Montserrat Puiggròs
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Alvaro Ferriz
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Asier Gonzalez
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Ivo Gut
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | | | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Romina Royo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Philippe Hupé
- Institut Curie, Paris, France; U900, Paris, France; PSL Research University, Paris, France; Mines Paris Tech, Fontainebleau, France; UMR144, CNRS, Paris, France
| | - David Torrents
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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VanSant-Webb C, Low HK, Kuramoto J, Stanley CE, Qiang H, Su AY, Ross AN, Cooper CG, Cox JE, Summers SA, Evason KJ, Ducker GS. Phospholipid isotope tracing suggests β-catenin-driven suppression of phosphatidylcholine metabolism in hepatocellular carcinoma. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159514. [PMID: 38795827 DOI: 10.1016/j.bbalip.2024.159514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/08/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Activating mutations in the CTNNB1 gene encoding β-catenin are among the most frequently observed oncogenic alterations in hepatocellular carcinoma (HCC). Profound alterations in lipid metabolism, including increases in fatty acid oxidation and transformation of the phospholipidome, occur in HCC with CTNNB1 mutations, but it is unclear what mechanisms give rise to these changes. We employed untargeted lipidomics and targeted isotope tracing to measure phospholipid synthesis activity in an inducible human liver cell line expressing mutant β-catenin, as well as in transgenic zebrafish with activated β-catenin-driven HCC. In both models, activated β-catenin expression was associated with large changes in the lipidome including conserved increases in acylcarnitines and ceramides and decreases in triglycerides. Lipid isotope tracing analysis in human cells revealed a reduction in phosphatidylcholine (PC) production rates as assayed by choline incorporation. We developed lipid isotope tracing analysis for zebrafish tumors and observed reductions in phosphatidylcholine synthesis by both the CDP-choline and PEMT pathways. The observed changes in the β-catenin-driven HCC phospholipidome suggest that zebrafish can recapitulate conserved features of HCC lipid metabolism and may serve as a model for identifying future HCC-specific lipid metabolic targets.
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Affiliation(s)
- Chad VanSant-Webb
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Hayden K Low
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Junko Kuramoto
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Claire E Stanley
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Hantao Qiang
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Audrey Y Su
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexis N Ross
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Chad G Cooper
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Scott A Summers
- Department of Nutrition and Integrative Physiology, University of Utah College of Health, Salt Lake City, UT 84112, USA
| | - Kimberley J Evason
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Gregory S Ducker
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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4
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Wang JR, Zafereo ME, Cabanillas ME, Wu CC, Xu L, Dai Y, Wang W, Lai SY, Henderson Y, Erasmus L, Williams MD, Joshu C, Ray D. The association between thyroid differentiation score and survival outcomes in papillary thyroid carcinoma. J Clin Endocrinol Metab 2024:dgae532. [PMID: 39087944 DOI: 10.1210/clinem/dgae532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/17/2024] [Accepted: 07/30/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Thyroid differentiation score (TDS), calculated based on mRNA expression levels of 16 genes controlling thyroid metabolism and function, has been proposed as a measure to quantify differentiation in PTC. The objective of this study is to determine whether TDS is associated with survival outcomes across patient cohorts. METHODS Two independent cohorts of PTC patients were used: 1) the Cancer Genome Atlas (TCGA) thyroid cancer study (N=372), 2) MD Anderson Cancer Center (MDACC) cohort (N=111). The primary survival outcome of interest was progression-free interval (PFI). Association with overall survival (OS) was also explored. The Kaplan-Meier method and Cox proportional hazards models were used for survival analyses. RESULTS In both cohorts, TDS was associated with tumor and nodal stage at diagnosis as well as tumor driver mutation status. High TDS was associated with longer PFI on univariable analyses across cohorts. After adjusting for overall stage, TDS remained significantly associated with PFI in the MDACC cohort only (aHR 0.67, 95%CI 0.52-0.85). In subgroup analyses stratified by tumor driver mutation status, higher TDS was most consistently associated with longer PFI in BRAFV600E-mutated tumors across cohorts after adjusting for overall stage (TCGA: aHR 0.60, 95% CI: 0.33-1.07; MDACC: aHR 0.59, 95% CI: 0.42-0.82). For OS, increasing TDS was associated with longer OS in the overall MDACC cohort (aHR=0.78, 95% CI:0.63-0.96), where the median duration of follow-up was 12.9 years. CONCLUSION TDS quantifies the spectrum of differentiation status in PTC and may serve as a potential prognostic biomarker in PTC, mostly promisingly in BRAFV600E-mutated tumors.
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Affiliation(s)
- Jennifer R Wang
- Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Mark E Zafereo
- Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Maria E Cabanillas
- Department of Endocrine Neoplasia & Hormonal Disorders, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chia Chin Wu
- Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Li Xu
- Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yaoyi Dai
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stephen Y Lai
- Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ying Henderson
- Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lauren Erasmus
- Department of Head and Neck Surgery, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michelle D Williams
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Corinne Joshu
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX
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5
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Atzeni R, Massidda M, Pieroni E, Rallo V, Pisu M, Angius A. A Novel Affordable and Reliable Framework for Accurate Detection and Comprehensive Analysis of Somatic Mutations in Cancer. Int J Mol Sci 2024; 25:8044. [PMID: 39125613 PMCID: PMC11311285 DOI: 10.3390/ijms25158044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Accurate detection and analysis of somatic variants in cancer involve multiple third-party tools with complex dependencies and configurations, leading to laborious, error-prone, and time-consuming data conversions. This approach lacks accuracy, reproducibility, and portability, limiting clinical application. Musta was developed to address these issues as an end-to-end pipeline for detecting, classifying, and interpreting cancer mutations. Musta is based on a Python command-line tool designed to manage tumor-normal samples for precise somatic mutation analysis. The core is a Snakemake-based workflow that covers all key cancer genomics steps, including variant calling, mutational signature deconvolution, variant annotation, driver gene detection, pathway analysis, and tumor heterogeneity estimation. Musta is easy to install on any system via Docker, with a Makefile handling installation, configuration, and execution, allowing for full or partial pipeline runs. Musta has been validated at the CRS4-NGS Core facility and tested on large datasets from The Cancer Genome Atlas and the Beijing Institute of Genomics. Musta has proven robust and flexible for somatic variant analysis in cancer. It is user-friendly, requiring no specialized programming skills, and enables data processing with a single command line. Its reproducibility ensures consistent results across users following the same protocol.
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Affiliation(s)
- Rossano Atzeni
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09050 Pula, Italy; (R.A.); (E.P.); (M.P.)
| | - Matteo Massidda
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Enrico Pieroni
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09050 Pula, Italy; (R.A.); (E.P.); (M.P.)
| | - Vincenzo Rallo
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy;
| | - Massimo Pisu
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09050 Pula, Italy; (R.A.); (E.P.); (M.P.)
| | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy;
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Hong X, Zhang X, Jiang R, Qiao S, Wang W, Zhang H, Wang J, Yin B, Li F, Ling C, Wang X, Zhao Y, Wu K, Wu W. A cross-species transcriptomic analysis reveals a novel 2-dimensional classification system explaining the invasiveness heterogeneity of pancreatic neuroendocrine tumor. Cancer Lett 2024:217131. [PMID: 39048044 DOI: 10.1016/j.canlet.2024.217131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/02/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
Pancreatic neuroendocrine tumors (PanNETs), the second most common type of primary pancreatic tumors, display notable heterogeneity in invasiveness. Current knowledge regarding genomic alterations, including DAXX/ATRX, MEN1 mutations, and copy number variations (CNVs), provides some insights into tumor invasiveness. However, the underlying reasons for the significant variation in invasiveness between insulinoma and other types of PanNETs remain unclear. To construct a comprehensive model for the stratification of prognosis, we employed analysis of both the well-established Rip1-Tag2 (RT2) mouse model of PanNETs and human PanNETs with various functional types. Firstly, by applying single-cell and bulk RNA sequencing in PanNETs from different ages and strains of RT2 mice and human PanNETs, we introduced a 2-dimensional (2D) classification system. Based on the 2-D classification system, human PanNETs were mainly classified as benign insulinomas or non-insulinomas subclusters. Non-insulinomas subtypes mainly included gastrinomas, glucagonomas, VIPomas, and NF-PanNETs, which all exhibited potential invasiveness. In addition, we discovered an enrichment of specific CNV patterns and mutations in corresponding human PanNET subclusters. Then we denoted somatic DAXX/ATRX as the 'second hit' and confounding factors for invasiveness. Finally, by combining the 2D system, DAXX/ATRX mutation status, and tumor diameter, a group of indolent PanNETs with minimal recurrence risk was identified. In conclusion, our current work constructed a comprehensive model to elucidate the heterogeneity of invasiveness in PanNETs and improve prognostic stratification.
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Affiliation(s)
- Xiafei Hong
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Xingwu Zhang
- Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Rui Jiang
- Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; Department of General Surgery, Xuanwu hospital capital medical university, Beijing, 100053, China
| | - Sitan Qiao
- BGI-Shenzhen, Shenzhen 518083, China; The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region of China
| | - Wenze Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Hao Zhang
- Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Jingqiao Wang
- Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Bohui Yin
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | | | - Chao Ling
- The Laboratory of Clinical Genetics, Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences& Peking Union Medical, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Xianze Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Kui Wu
- BGI-Shenzhen, Shenzhen 518083, China.
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
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7
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Min Q, Zhang M, Lin D, Zhang W, Li X, Zhao L, Teng H, He T, Sun W, Fan J, Yu X, Chen J, Li J, Gao X, Dong B, Liu R, Liu X, Song Y, Cui Y, Lu SH, Li R, Guo M, Wang Y, Zhan Q. Genomic characterization and risk stratification of esophageal squamous dysplasia. MEDICAL REVIEW (2021) 2024; 4:244-256. [PMID: 38919397 PMCID: PMC11195426 DOI: 10.1515/mr-2024-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Objectives The majority of esophageal squamous dysplasia (ESD) patients progress slowly, while a subset of patients can undergo recurrence rapidly or progress to invasive cancer even after proper treatment. However, the molecular mechanisms underlying these clinical observations are still largely unknown. Methods By sequencing the genomic data of 160 clinical samples from 49 tumor-free ESD patients and 88 esophageal squamous cell carcinoma (ESCC) patients, we demonstrated lower somatic mutation and copy number alteration (CNA) burden in ESD compared with ESCC. Results Cross-species screening and functional assays identified ACSM5 as a novel driver gene for ESD progression. Furthermore, we revealed that miR-4292 promoted ESD progression and could serve as a non-invasive diagnostic marker for ESD. Conclusions These findings largely expanded our understanding of ESD genetics and tumorigenesis, which possessed promising significance for improving early diagnosis, reducing overtreatment, and identifying high-risk ESD patients.
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Affiliation(s)
- Qingjie Min
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | | | - Dongmei Lin
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Weimin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xianfeng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- Department of Gastroenterology, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lianmei Zhao
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Tao He
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
- Department of Pathology, Characteristic Medical Center of Chinese People’s Armed Police Force, Tianjin, China
| | - Wei Sun
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiawen Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiying Yu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jinting Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaohan Gao
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Dong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Central Laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Rui Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xuefeng Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongping Cui
- Shenzhen Peking University-The Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Shih-Hsin Lu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- Peking University International Cancer Institute, Peking University, Beijing, China
- Soochow University Cancer Institute, Suzhou, China
- State Key Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
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8
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Ji S, Zhu T, Sethia A, Wang W. Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples. Genome Res 2024; 34:633-641. [PMID: 38589250 PMCID: PMC11146589 DOI: 10.1101/gr.278456.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
Accurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenges were overcome by consensus mutation calling from four to five popular callers. This, however, increases the already nontrivial computing time from individual callers. Here, we launch MuSE 2, powered by multistep parallelization and efficient memory allocation, to resolve the computing time bottleneck. MuSE 2 speeds up 50 times more than MuSE 1 and eight to 80 times more than other popular callers. Our benchmark study suggests combining MuSE 2 and the recently accelerated Strelka2 achieves high efficiency and accuracy in analyzing large cancer genomic data sets.
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Affiliation(s)
- Shuangxi Ji
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Tong Zhu
- NVIDIA Corporation, Santa Clara, California 95051, USA
| | - Ankit Sethia
- NVIDIA Corporation, Santa Clara, California 95051, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
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9
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Muyas F, Sauer CM, Valle-Inclán JE, Li R, Rahbari R, Mitchell TJ, Hormoz S, Cortés-Ciriano I. De novo detection of somatic mutations in high-throughput single-cell profiling data sets. Nat Biotechnol 2024; 42:758-767. [PMID: 37414936 PMCID: PMC11098751 DOI: 10.1038/s41587-023-01863-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Characterization of somatic mutations at single-cell resolution is essential to study cancer evolution, clonal mosaicism and cell plasticity. Here, we describe SComatic, an algorithm designed for the detection of somatic mutations in single-cell transcriptomic and ATAC-seq (assay for transposase-accessible chromatin sequence) data sets directly without requiring matched bulk or single-cell DNA sequencing data. SComatic distinguishes somatic mutations from polymorphisms, RNA-editing events and artefacts using filters and statistical tests parameterized on non-neoplastic samples. Using >2.6 million single cells from 688 single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) data sets spanning cancer and non-neoplastic samples, we show that SComatic detects mutations in single cells accurately, even in differentiated cells from polyclonal tissues that are not amenable to mutation detection using existing methods. Validated against matched genome sequencing and scRNA-seq data, SComatic achieves F1 scores between 0.6 and 0.7 across diverse data sets, in comparison to 0.2-0.4 for the second-best performing method. In summary, SComatic permits de novo mutational signature analysis, and the study of clonal heterogeneity and mutational burdens at single-cell resolution.
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Affiliation(s)
- Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Carolin M Sauer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Ruoyan Li
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Raheleh Rahbari
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas J Mitchell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Sahand Hormoz
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.
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10
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Ramakrishnan S, Cortes-Gomez E, Athans SR, Attwood KM, Rosario SR, Kim SJ, Mager DE, Isenhart EG, Hu Q, Wang J, Woloszynska A. Race-specific coregulatory and transcriptomic profiles associated with DNA methylation and androgen receptor in prostate cancer. Genome Med 2024; 16:52. [PMID: 38566104 PMCID: PMC10988846 DOI: 10.1186/s13073-024-01323-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Prostate cancer is a significant health concern, particularly among African American (AA) men who exhibit higher incidence and mortality compared to European American (EA) men. Understanding the molecular mechanisms underlying these disparities is imperative for enhancing clinical management and achieving better outcomes. METHODS Employing a multi-omics approach, we analyzed prostate cancer in both AA and EA men. Using Illumina methylation arrays and RNA sequencing, we investigated DNA methylation and gene expression in tumor and non-tumor prostate tissues. Additionally, Boolean analysis was utilized to unravel complex networks contributing to racial disparities in prostate cancer. RESULTS When comparing tumor and adjacent non-tumor prostate tissues, we found that DNA hypermethylated regions are enriched for PRC2/H3K27me3 pathways and EZH2/SUZ12 cofactors. Olfactory/ribosomal pathways and distinct cofactors, including CTCF and KMT2A, were enriched in DNA hypomethylated regions in prostate tumors from AA men. We identified race-specific inverse associations of DNA methylation with expression of several androgen receptor (AR) associated genes, including the GATA family of transcription factors and TRIM63. This suggests that race-specific dysregulation of the AR signaling pathway exists in prostate cancer. To investigate the effect of AR inhibition on race-specific gene expression changes, we generated in-silico patient-specific prostate cancer Boolean networks. Our simulations revealed prolonged AR inhibition causes significant dysregulation of TGF-β, IDH1, and cell cycle pathways specifically in AA prostate cancer. We further quantified global gene expression changes, which revealed differential expression of genes related to microtubules, immune function, and TMPRSS2-fusion pathways, specifically in prostate tumors of AA men. Enrichment of these pathways significantly correlated with an altered risk of disease progression in a race-specific manner. CONCLUSIONS Our study reveals unique signaling networks underlying prostate cancer biology in AA and EA men, offering potential insights for clinical management strategies tailored to specific racial groups. Targeting AR and associated pathways could be particularly beneficial in addressing the disparities observed in prostate cancer outcomes in the context of AA and EA men. Further investigation into these identified pathways may lead to the development of personalized therapeutic approaches to improve outcomes for prostate cancer patients across different racial backgrounds.
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Affiliation(s)
- Swathi Ramakrishnan
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Eduardo Cortes-Gomez
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Biostatistics, SUNY University at Buffalo, Kimball Tower, Buffalo, NY, 14214, USA
| | - Sarah R Athans
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Kristopher M Attwood
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Spencer R Rosario
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Se Jin Kim
- Department of Pharmaceutical Sciences, SUNY University at Buffalo, Buffalo, NY, 14214, USA
| | - Donald E Mager
- Department of Pharmaceutical Sciences, SUNY University at Buffalo, Buffalo, NY, 14214, USA
- Enhanced Pharmacodynamics, LLC, Buffalo, NY, 14203, USA
| | - Emily G Isenhart
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Qiang Hu
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Jianmin Wang
- Department of Bioinformatics and Biostatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Anna Woloszynska
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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11
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De Battista D, Yakymi R, Scheibe E, Sato S, Gerstein H, Markowitz TE, Lack J, Mereu R, Manieli C, Zamboni F, Farci P. Identification of Two Distinct Immune Subtypes in Hepatitis B Virus (HBV)-Associated Hepatocellular Carcinoma (HCC). Cancers (Basel) 2024; 16:1370. [PMID: 38611048 PMCID: PMC11011136 DOI: 10.3390/cancers16071370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/12/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
HBV is the most common risk factor for HCC development, accounting for almost 50% of cases worldwide. Despite significant advances in immunotherapy, there is limited information on the HBV-HCC tumor microenvironment (TME), which may influence the response to checkpoint inhibitors. Here, we characterize the TME in a unique series of liver specimens from HBV-HCC patients to identify who might benefit from immunotherapy. By combining an extensive immunohistochemistry analysis with the transcriptomic profile of paired liver samples (tumor vs. nontumorous tissue) from 12 well-characterized Caucasian patients with HBV-HCC, we identified two distinct tumor subtypes that we defined immune-high and immune-low. The immune-high subtype, seen in half of the patients, is characterized by a high number of infiltrating B and T cells in association with stromal activation and a transcriptomic profile featuring inhibition of antigen presentation and CTL activation. All the immune-high tumors expressed high levels of CTLA-4 and low levels of PD-1, while PD-L1 was present only in four of six cases. In contrast, the immune-low subtype shows significantly lower lymphocyte infiltration and stromal activation. By whole exome sequencing, we documented that four out of six individuals with the immune-low subtype had missense mutations in the CTNNB1 gene, while only one patient had mutations in this gene in the immune-high subtype. Outside the tumor, there were no differences between the two subtypes. This study identifies two distinctive immune subtypes in HBV-associated HCC, regardless of the microenvironment observed in the surrounding nontumorous tissue, providing new insights into pathogenesis. These findings may be instrumental in the identification of patients who might benefit from immunotherapy.
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Affiliation(s)
- Davide De Battista
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (D.D.B.); (R.Y.); (E.S.); (S.S.); (H.G.)
| | - Rylee Yakymi
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (D.D.B.); (R.Y.); (E.S.); (S.S.); (H.G.)
| | - Evangeline Scheibe
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (D.D.B.); (R.Y.); (E.S.); (S.S.); (H.G.)
| | - Shinya Sato
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (D.D.B.); (R.Y.); (E.S.); (S.S.); (H.G.)
| | - Hannah Gerstein
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (D.D.B.); (R.Y.); (E.S.); (S.S.); (H.G.)
| | - Tovah E. Markowitz
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Roberto Mereu
- Department of Surgery, Liver Transplantation Center, Azienda Ospedaliera Brotzu, 09047 Cagliari, Italy; (R.M.); (F.Z.)
| | - Cristina Manieli
- Sevizio di Anatomia Patologica, Azienda Ospedaliera Brotzu, 09047 Cagliari, Italy;
| | - Fausto Zamboni
- Department of Surgery, Liver Transplantation Center, Azienda Ospedaliera Brotzu, 09047 Cagliari, Italy; (R.M.); (F.Z.)
| | - Patrizia Farci
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (D.D.B.); (R.Y.); (E.S.); (S.S.); (H.G.)
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12
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Ergun MA, Cinal O, Bakışlı B, Emül AA, Baysan M. COSAP: Comparative Sequencing Analysis Platform. BMC Bioinformatics 2024; 25:130. [PMID: 38532317 DOI: 10.1186/s12859-024-05756-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Recent improvements in sequencing technologies enabled detailed profiling of genomic features. These technologies mostly rely on short reads which are merged and compared to reference genome for variant identification. These operations should be done with computers due to the size and complexity of the data. The need for analysis software resulted in many programs for mapping, variant calling and annotation steps. Currently, most programs are either expensive enterprise software with proprietary code which makes access and verification very difficult or open-access programs that are mostly based on command-line operations without user interfaces and extensive documentation. Moreover, a high level of disagreement is observed among popular mapping and variant calling algorithms in multiple studies, which makes relying on a single algorithm unreliable. User-friendly open-source software tools that offer comparative analysis are an important need considering the growth of sequencing technologies. RESULTS Here, we propose Comparative Sequencing Analysis Platform (COSAP), an open-source platform that provides popular sequencing algorithms for SNV, indel, structural variant calling, copy number variation, microsatellite instability and fusion analysis and their annotations. COSAP is packed with a fully functional user-friendly web interface and a backend server which allows full independent deployment for both individual and institutional scales. COSAP is developed as a workflow management system and designed to enhance cooperation among scientists with different backgrounds. It is publicly available at https://cosap.bio and https://github.com/MBaysanLab/cosap/ . The source code of the frontend and backend services can be found at https://github.com/MBaysanLab/cosap-webapi/ and https://github.com/MBaysanLab/cosap_frontend/ respectively. All services are packed as Docker containers as well. Pipelines that combine algorithms can be customized and new algorithms can be added with minimal coding through modular structure. CONCLUSIONS COSAP simplifies and speeds up the process of DNA sequencing analyses providing commonly used algorithms for SNV, indel, structural variant calling, copy number variation, microsatellite instability and fusion analysis as well as their annotations. COSAP is packed with a fully functional user-friendly web interface and a backend server which allows full independent deployment for both individual and institutional scales. Standardized implementations of popular algorithms in a modular platform make comparisons much easier to assess the impact of alternative pipelines which is crucial in establishing reproducibility of sequencing analyses.
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Affiliation(s)
- Mehmet Arif Ergun
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Omer Cinal
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Berkant Bakışlı
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Abdullah Asım Emül
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Mehmet Baysan
- Department of Computer Engineering, Istanbul Technical University, 34469, Istanbul, Turkey.
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13
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Xue Y, Su Z, Lin X, Ho MK, Yu KHO. Single-cell lineage tracing with endogenous markers. Biophys Rev 2024; 16:125-139. [PMID: 38495438 PMCID: PMC10937880 DOI: 10.1007/s12551-024-01179-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/18/2024] [Indexed: 03/19/2024] Open
Abstract
Resolving lineage relationships between cells in an organism provides key insights into the fate of individual cells and drives a fundamental understanding of the process of development and disease. A recent rapid increase in experimental and computational advances for detecting naturally occurring somatic nuclear and mitochondrial mutation at single-cell resolution has expanded lineage tracing from model organisms to humans. This review discusses the advantages and challenges of experimental and computational techniques for cell lineage tracing using somatic mutation as endogenous DNA barcodes to decipher the relationships between cells during development and tumour evolution. We outlook the advantages of spatial clonal evolution analysis and single-cell lineage tracing using endogenous genetic markers.
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Affiliation(s)
- Yan Xue
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Units 1201-1206, 1223 & 1225, 12/F, Building 19W, 19 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Zezhuo Su
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Units 1201-1206, 1223 & 1225, 12/F, Building 19W, 19 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xinyi Lin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Mun Kay Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Ken H. O. Yu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Units 1201-1206, 1223 & 1225, 12/F, Building 19W, 19 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
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14
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Patel Y, Zhu C, Yamaguchi TN, Bugh YZ, Tian M, Holmes A, Fitz-Gibbon ST, Boutros PC. NFTest: automated testing of Nextflow pipelines. Bioinformatics 2024; 40:btae081. [PMID: 38341660 PMCID: PMC10881102 DOI: 10.1093/bioinformatics/btae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/18/2024] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
MOTIVATION The ongoing expansion in the volume of biomedical data has contributed to a growing complexity in the tools and technologies used in research with an increased reliance on complex workflows written in orchestration languages such as Nextflow to integrate algorithms into processing pipelines. The growing use of workflows involving various tools and algorithms has led to increased scrutiny of software development practices to avoid errors in individual tools and in the connections between them. RESULTS To facilitate test-driven development of Nextflow pipelines, we created NFTest, a framework for automated pipeline testing and validation with customizability options for Nextflow features. It is open-source, easy to initialize and use, and customizable to allow for testing of complex workflows with test success configurable through a broad range of assertions. NFTest simplifies the testing burden on developers by automating tests once defined and providing a flexible interface for running tests to validate workflows. This reduces the barrier to rigorous biomedical workflow testing and paves the way toward reducing computational errors in biomedicine. AVAILABILITY AND IMPLEMENTATION NFTest is an open-source Python framework under the GPLv2 license and is freely available at https://github.com/uclahs-cds/tool-NFTest. The call-sSNV Nextflow pipeline is available at: https://github.com/uclahs-cds/pipeline-call-sSNV.
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Affiliation(s)
- Yash Patel
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Chenghao Zhu
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Takafumi N Yamaguchi
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Yuan Zhe Bugh
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Mao Tian
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Aaron Holmes
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Sorel T Fitz-Gibbon
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Paul C Boutros
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Urology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA 90095, United States
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15
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Gulhan DC, Viswanadham V, Muyas F, Jin H, Foote MB, Lee JJK, Barras D, Jung YL, Ljungstrom V, Rousseau B, Galor A, Diplas BH, Maron SB, Cleary JM, Cortés-Ciriano I, Park PJ. Predicting response to immune checkpoint blockade therapy among mismatch repair-deficient patients using mutational signatures. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.19.24301236. [PMID: 38293061 PMCID: PMC10827269 DOI: 10.1101/2024.01.19.24301236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Despite the overall efficacy of immune checkpoint blockade (ICB) for mismatch repair deficiency (MMRD) across tumor types, a sizable fraction of patients with MMRD still do not respond to ICB. We performed mutational signature analysis of panel sequencing data (n = 95) from MMRD cases treated with ICB. We discover that T>C-rich single base substitution (SBS) signatures-SBS26 and SBS54 from the COSMIC Mutational Signatures catalog-identify MMRD patients with significantly shorter overall survival. Tumors with a high burden of SBS26 show over-expression and enriched mutations of genes involved in double-strand break repair and other DNA repair pathways. They also display chromosomal instability (CIN), likely related to replication fork instability, leading to copy number losses that trigger immune evasion. SBS54 is associated with transcriptional activity and not with CIN, defining a distinct subtype. Consistently, cancer cell lines with a high burden of SBS26 and SBS54 are sensitive to treatments targeting pathways related to their proposed etiology. Together, our analysis offers an explanation for the heterogeneous responses to ICB among MMRD patients and supports an SBS signature-based predictor as a prognostic biomarker for differential ICB response.
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16
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Dhanushkumar T, M E S, Selvam PK, Rambabu M, Dasegowda KR, Vasudevan K, George Priya Doss C. Advancements and hurdles in the development of a vaccine for triple-negative breast cancer: A comprehensive review of multi-omics and immunomics strategies. Life Sci 2024; 337:122360. [PMID: 38135117 DOI: 10.1016/j.lfs.2023.122360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Triple-Negative Breast Cancer (TNBC) presents a significant challenge in oncology due to its aggressive behavior and limited therapeutic options. This review explores the potential of immunotherapy, particularly vaccine-based approaches, in addressing TNBC. It delves into the role of immunoinformatics in creating effective vaccines against TNBC. The review first underscores the distinct attributes of TNBC and the importance of tumor antigens in vaccine development. It then elaborates on antigen detection techniques such as exome sequencing, HLA typing, and RNA sequencing, which are instrumental in identifying TNBC-specific antigens and selecting vaccine candidates. The discussion then shifts to the in-silico vaccine development process, encompassing antigen selection, epitope prediction, and rational vaccine design. This process merges computational simulations with immunological insights. The role of Artificial Intelligence (AI) in expediting the prediction of antigens and epitopes is also emphasized. The review concludes by encapsulating how Immunoinformatics can augment the design of TNBC vaccines, integrating tumor antigens, advanced detection methods, in-silico strategies, and AI-driven insights to advance TNBC immunotherapy. This could potentially pave the way for more targeted and efficacious treatments.
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Affiliation(s)
- T Dhanushkumar
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Santhosh M E
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Prasanna Kumar Selvam
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Majji Rambabu
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - K R Dasegowda
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
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17
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Yang X, Huang K, Yang D, Zhao W, Zhou X. Biomedical Big Data Technologies, Applications, and Challenges for Precision Medicine: A Review. GLOBAL CHALLENGES (HOBOKEN, NJ) 2024; 8:2300163. [PMID: 38223896 PMCID: PMC10784210 DOI: 10.1002/gch2.202300163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/20/2023] [Indexed: 01/16/2024]
Abstract
The explosive growth of biomedical Big Data presents both significant opportunities and challenges in the realm of knowledge discovery and translational applications within precision medicine. Efficient management, analysis, and interpretation of big data can pave the way for groundbreaking advancements in precision medicine. However, the unprecedented strides in the automated collection of large-scale molecular and clinical data have also introduced formidable challenges in terms of data analysis and interpretation, necessitating the development of novel computational approaches. Some potential challenges include the curse of dimensionality, data heterogeneity, missing data, class imbalance, and scalability issues. This overview article focuses on the recent progress and breakthroughs in the application of big data within precision medicine. Key aspects are summarized, including content, data sources, technologies, tools, challenges, and existing gaps. Nine fields-Datawarehouse and data management, electronic medical record, biomedical imaging informatics, Artificial intelligence-aided surgical design and surgery optimization, omics data, health monitoring data, knowledge graph, public health informatics, and security and privacy-are discussed.
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Affiliation(s)
- Xue Yang
- Department of Pancreatic Surgery and West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengdu610041China
| | - Kexin Huang
- Department of Pancreatic Surgery and West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengdu610041China
| | - Dewei Yang
- College of Advanced Manufacturing EngineeringChongqing University of Posts and TelecommunicationsChongqingChongqing400000China
| | - Weiling Zhao
- Center for Systems MedicineSchool of Biomedical InformaticsUTHealth at HoustonHoustonTX77030USA
| | - Xiaobo Zhou
- Center for Systems MedicineSchool of Biomedical InformaticsUTHealth at HoustonHoustonTX77030USA
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18
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Speer RM, Nandi SP, Cooper KL, Zhou X, Yu H, Guo Y, Hudson LG, Alexandrov LB, Liu KJ. Arsenic is a potent co-mutagen of ultraviolet light. Commun Biol 2023; 6:1273. [PMID: 38104187 PMCID: PMC10725444 DOI: 10.1038/s42003-023-05659-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
Arsenic enhances the carcinogenicity of ultraviolet radiation (UVR). However, the mechanisms of arsenic-driven oncogenesis are not well understood. Here, we utilize experimental systems to investigate the carcinogenic and mutagenic properties of co-exposure to arsenic and UVR. In vitro and in vivo exposures indicate that, by itself, arsenic is not mutagenic. However, in combination with UVR, arsenic exposure has a synergistic effect leading to an accelerated mouse skin carcinogenesis and to more than 2-fold enrichment of UVR mutational burden. Notably, mutational signature ID13, previously found only in UVR-associated human skin cancers, is observed exclusively in mouse skin tumors and cell lines jointly exposed to arsenic and UVR. This signature was not observed in any model system exposed purely to arsenic or purely to UVR, making ID13, to the best of our knowledge, the first co-exposure signature to be reported using controlled experimental conditions. Analysis of existing skin cancer genomics data reveals that only a subset of cancers harbor ID13 and these exhibit an elevated UVR mutagenesis. Our results report a unique mutational signature caused by a co-exposure to two environmental carcinogens and provide comprehensive evidence that arsenic is a potent co-mutagen and co-carcinogen of UVR.
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Affiliation(s)
- Rachel M Speer
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Shuvro P Nandi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
| | - Karen L Cooper
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Xixi Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Hui Yu
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA
| | - Yan Guo
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA.
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.
| | - Ke Jian Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, 87106, USA.
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, 11794, USA.
- Department of Pathology, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA.
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19
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Fitzpatrick A, Iravani M, Mills A, Vicente D, Alaguthurai T, Roxanis I, Turner NC, Haider S, Tutt ANJ, Isacke CM. Genomic profiling and pre-clinical modelling of breast cancer leptomeningeal metastasis reveals acquisition of a lobular-like phenotype. Nat Commun 2023; 14:7408. [PMID: 37973922 PMCID: PMC10654396 DOI: 10.1038/s41467-023-43242-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Breast cancer leptomeningeal metastasis (BCLM), where tumour cells grow along the lining of the brain and spinal cord, is a devastating development for patients. Investigating this metastatic site is hampered by difficulty in accessing tumour material. Here, we utilise cerebrospinal fluid (CSF) cell-free DNA (cfDNA) and CSF disseminated tumour cells (DTCs) to explore the clonal evolution of BCLM and heterogeneity between leptomeningeal and extracranial metastatic sites. Somatic alterations with potential therapeutic actionability were detected in 81% (17/21) of BCLM cases, with 19% detectable in CSF cfDNA only. BCLM was enriched in genomic aberrations in adherens junction and cytoskeletal genes, revealing a lobular-like breast cancer phenotype. CSF DTCs were cultured in 3D to establish BCLM patient-derived organoids, and used for the successful generation of BCLM in vivo models. These data reveal that BCLM possess a unique genomic aberration profile and highlight potential cellular dependencies in this hard-to-treat form of metastatic disease.
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Affiliation(s)
- Amanda Fitzpatrick
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, King's College London, London, UK
| | - Marjan Iravani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Adam Mills
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - David Vicente
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Nicholas C Turner
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Andrew N J Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Breast Cancer Now Research Unit, Guy's Hospital, King's College London, London, UK
- Oncology and Haematology Directorate, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Clare M Isacke
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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20
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VanSant-Webb C, Low HK, Kuramoto J, Stanley CE, Qiang H, Su A, Ross AN, Cooper CG, Cox JE, Summers SA, Evason KJ, Ducker GS. Phospholipid isotope tracing reveals β-catenin-driven suppression of phosphatidylcholine metabolism in hepatocellular carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.12.562134. [PMID: 37904922 PMCID: PMC10614757 DOI: 10.1101/2023.10.12.562134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Background and Aims Activating mutations in the CTNNB1 gene encoding β-catenin are among the most frequently observed oncogenic alterations in hepatocellular carcinoma (HCC). HCC with CTNNB1 mutations show profound alterations in lipid metabolism including increases in fatty acid oxidation and transformation of the phospholipidome, but it is unclear how these changes arise and whether they contribute to the oncogenic program in HCC. Methods We employed untargeted lipidomics and targeted isotope tracing to quantify phospholipid production fluxes in an inducible human liver cell line expressing mutant β-catenin, as well as in transgenic zebrafish with activated β-catenin-driven HCC. Results In both models, activated β-catenin expression was associated with large changes in the lipidome including conserved increases in acylcarnitines and ceramides and decreases in triglycerides. Lipid flux analysis in human cells revealed a large reduction in phosphatidylcholine (PC) production rates as assayed by choline tracer incorporation. We developed isotope tracing lipid flux analysis for zebrafish and observed similar reductions in phosphatidylcholine synthesis flux accomplished by sex-specific mechanisms. Conclusions The integration of isotope tracing with lipid abundances highlights specific lipid class transformations downstream of β-catenin signaling in HCC and suggests future HCC-specific lipid metabolic targets.
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Affiliation(s)
- Chad VanSant-Webb
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Hayden K Low
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Junko Kuramoto
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Claire E Stanley
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Hantao Qiang
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Audrey Su
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Alexis N Ross
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Chad G Cooper
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
| | - Scott A Summers
- Department of Nutrition and Integrative Physiology, University of Utah College of Health. Salt Lake City, UT 84112 USA
| | - Kimberley J Evason
- Department of Pathology, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
- Huntsman Cancer Institute, University of Utah. Salt Lake City UT, 84112 USA
| | - Gregory S Ducker
- Department of Biochemistry, University of Utah School of Medicine. Salt Lake City UT, 84112, USA
- Huntsman Cancer Institute, University of Utah. Salt Lake City UT, 84112 USA
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21
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Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, Blanc E, Szymansky A, Hertwig F, Ishaque N, Beule D, Torrents D, Eggert A, Koche RP, Schwarz RF, Haase K, Schulte JH, Henssen AG. Mutational topography reflects clinical neuroblastoma heterogeneity. CELL GENOMICS 2023; 3:100402. [PMID: 37868040 PMCID: PMC10589636 DOI: 10.1016/j.xgen.2023.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 10/24/2023]
Abstract
Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.
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Affiliation(s)
- Elias Rodriguez-Fos
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mercè Planas-Fèlix
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nina Thiessen
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Eric Blanc
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Angelika Eggert
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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22
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Westcott PMK, Muyas F, Hauck H, Smith OC, Sacks NJ, Ely ZA, Jaeger AM, Rideout WM, Zhang D, Bhutkar A, Beytagh MC, Canner DA, Jaramillo GC, Bronson RT, Naranjo S, Jin A, Patten JJ, Cruz AM, Shanahan SL, Cortes-Ciriano I, Jacks T. Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity. Nat Genet 2023; 55:1686-1695. [PMID: 37709863 PMCID: PMC10562252 DOI: 10.1038/s41588-023-01499-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
DNA mismatch repair deficiency (MMRd) is associated with a high tumor mutational burden (TMB) and sensitivity to immune checkpoint blockade (ICB) therapy. Nevertheless, most MMRd tumors do not durably respond to ICB and critical questions remain about immunosurveillance and TMB in these tumors. In the present study, we developed autochthonous mouse models of MMRd lung and colon cancer. Surprisingly, these models did not display increased T cell infiltration or ICB response, which we showed to be the result of substantial intratumor heterogeneity of mutations. Furthermore, we found that immunosurveillance shapes the clonal architecture but not the overall burden of neoantigens, and T cell responses against subclonal neoantigens are blunted. Finally, we showed that clonal, but not subclonal, neoantigen burden predicts ICB response in clinical trials of MMRd gastric and colorectal cancer. These results provide important context for understanding immune evasion in cancers with a high TMB and have major implications for therapies aimed at increasing TMB.
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Affiliation(s)
- Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Haley Hauck
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Olivia C Smith
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nathan J Sacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zackery A Ely
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex M Jaeger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel Zhang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arjun Bhutkar
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mary C Beytagh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David A Canner
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Grissel C Jaramillo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Abbey Jin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J J Patten
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amanda M Cruz
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sean-Luc Shanahan
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Rodent Histopathology Core, Harvard Medical School, Boston, MA, USA.
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23
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Zhang B, Bassani-Sternberg M. Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery. J Immunother Cancer 2023; 11:e007073. [PMID: 37899131 PMCID: PMC10619091 DOI: 10.1136/jitc-2023-007073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2023] [Indexed: 10/31/2023] Open
Abstract
Identification of tumor antigens presented by the human leucocyte antigen (HLA) molecules is essential for the design of effective and safe cancer immunotherapies that rely on T cell recognition and killing of tumor cells. Mass spectrometry (MS)-based immunopeptidomics enables high-throughput, direct identification of HLA-bound peptides from a variety of cell lines, tumor tissues, and healthy tissues. It involves immunoaffinity purification of HLA complexes followed by MS profiling of the extracted peptides using data-dependent acquisition, data-independent acquisition, or targeted approaches. By incorporating DNA, RNA, and ribosome sequencing data into immunopeptidomics data analysis, the proteogenomic approach provides a powerful means for identifying tumor antigens encoded within the canonical open reading frames of annotated coding genes and non-canonical tumor antigens derived from presumably non-coding regions of our genome. We discuss emerging computational challenges in immunopeptidomics data analysis and tumor antigen identification, highlighting key considerations in the proteogenomics-based approach, including accurate DNA, RNA and ribosomal sequencing data analysis, careful incorporation of predicted novel protein sequences into reference protein database, special quality control in MS data analysis due to the expanded and heterogeneous search space, cancer-specificity determination, and immunogenicity prediction. The advancements in technology and computation is continually enabling us to identify tumor antigens with higher sensitivity and accuracy, paving the way toward the development of more effective cancer immunotherapies.
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Affiliation(s)
- Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Cancer Research Centre, Lausanne, Switzerland
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24
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Bolivar AM, Duzagac F, Sinha KM, Vilar E. Advances in vaccine development for cancer prevention and treatment in Lynch Syndrome. Mol Aspects Med 2023; 93:101204. [PMID: 37478804 PMCID: PMC10528439 DOI: 10.1016/j.mam.2023.101204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
Lynch Syndrome (LS) is one of the most common hereditary cancer syndromes, and is caused by mutations in one of the four DNA mismatch repair (MMR) genes, namely MLH1, MSH2, MSH6 and PMS2. Tumors developed by LS carriers display high levels of microsatellite instability, which leads to the accumulation of large numbers of mutations, among which frameshift insertion/deletions (indels) within microsatellite (MS) loci are the most common. As a result, MMR-deficient (MMRd) cells generate increased rates of tumor-specific neoantigens (neoAgs) that can be recognized by the immune system to activate cancer cell killing. In this context, LS is an ideal disease to leverage immune-interception strategies. Therefore, the identification of these neoAgs is an ongoing effort for the development of LS cancer preventive vaccines. In this review, we summarize the computational methods used for in silico neoAg prediction, including their challenges, and the experimental techniques used for in vitro validation of their immunogenicity. In addition, we outline results from past and on-going vaccine clinical trials and highlight avenues for improvement and future directions.
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Affiliation(s)
- Ana M Bolivar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fahriye Duzagac
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krishna M Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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25
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O’Sullivan B, Seoighe C. Comprehensive and realistic simulation of tumour genomic sequencing data. NAR Cancer 2023; 5:zcad051. [PMID: 37746635 PMCID: PMC10516706 DOI: 10.1093/narcan/zcad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Accurate identification of somatic mutations and allele frequencies in cancer has critical research and clinical applications. Several computational tools have been developed for this purpose but, in the absence of comprehensive 'ground truth' data, assessing the accuracy of these methods is challenging. We created a computational framework to simulate tumour and matched normal sequencing data for which the source of all loci that contain non-reference bases is known, based on a phased, personalized genome. Unlike existing methods, we account for sampling errors inherent in the sequencing process. Using this framework, we assess accuracy and biases in inferred mutations and their frequencies in an established somatic mutation calling pipeline. We demonstrate bias in existing methods of mutant allele frequency estimation and show, for the first time, the observed mutation frequency spectrum corresponding to a theoretical model of tumour evolution. We highlight the impact of quality filters on detection sensitivity of clinically actionable variants and provide definitive assessment of false positive and false negative mutation calls. Our simulation framework provides an improved means to assess the accuracy of somatic mutation calling pipelines and a detailed picture of the effects of technical parameters and experimental factors on somatic mutation calling in cancer samples.
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Affiliation(s)
- Brian O’Sullivan
- School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
| | - Cathal Seoighe
- School of Mathematical and Statistical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
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26
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Schuster SL, Arora S, Wladyka CL, Itagi P, Corey L, Young D, Stackhouse BL, Kollath L, Wu QV, Corey E, True LD, Ha G, Paddison PJ, Hsieh AC. Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3' untranslated region mutations. Cell Rep 2023; 42:112840. [PMID: 37516102 PMCID: PMC10540565 DOI: 10.1016/j.celrep.2023.112840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/05/2023] [Accepted: 07/05/2023] [Indexed: 07/31/2023] Open
Abstract
3' untranslated region (3' UTR) somatic mutations represent a largely unexplored avenue of alternative oncogenic gene dysregulation. To determine the significance of 3' UTR mutations in disease, we identify 3' UTR somatic variants across 185 advanced prostate tumors, discovering 14,497 single-nucleotide mutations enriched in oncogenic pathways and 3' UTR regulatory elements. By developing two complementary massively parallel reporter assays, we measure how thousands of patient-based mutations affect mRNA translation and stability and identify hundreds of functional variants that allow us to define determinants of mutation significance. We demonstrate the clinical relevance of these mutations, observing that CRISPR-Cas9 endogenous editing of distinct variants increases cellular stress resistance and that patients harboring oncogenic 3' UTR mutations have a particularly poor prognosis. This work represents an expansive view of the extent to which disease-relevant 3' UTR mutations affect mRNA stability, translation, and cancer progression, uncovering principles of regulatory functionality and potential therapeutic targets in previously unexplored regulatory regions.
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Affiliation(s)
- Samantha L Schuster
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Cynthia L Wladyka
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Pushpa Itagi
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lukas Corey
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Dave Young
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Lori Kollath
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Qian V Wu
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Gavin Ha
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Patrick J Paddison
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew C Hsieh
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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27
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Isidro-Hernández M, Casado-García A, Oak N, Alemán-Arteaga S, Ruiz-Corzo B, Martínez-Cano J, Mayado A, Sánchez EG, Blanco O, Gaspar ML, Orfao A, Alonso-López D, De Las Rivas J, Riesco S, Prieto-Matos P, González-Murillo Á, Criado FJG, Cenador MBG, Ramírez-Orellana M, de Andrés B, Vicente-Dueñas C, Cobaleda C, Nichols KE, Sánchez-García I. Immune stress suppresses innate immune signaling in preleukemic precursor B-cells to provoke leukemia in predisposed mice. Nat Commun 2023; 14:5159. [PMID: 37620322 PMCID: PMC10449887 DOI: 10.1038/s41467-023-40961-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
The initial steps of B-cell acute lymphoblastic leukemia (B-ALL) development usually pass unnoticed in children. Several preclinical studies have shown that exposure to immune stressors triggers the transformation of preleukemic B cells to full-blown B-ALL, but how this takes place is still a longstanding and unsolved challenge. Here we show that dysregulation of innate immunity plays a driving role in the clonal evolution of pre-malignant Pax5+/- B-cell precursors toward leukemia. Transcriptional profiling reveals that Myd88 is downregulated in immune-stressed pre-malignant B-cell precursors and in leukemic cells. Genetic reduction of Myd88 expression leads to a significant increase in leukemia incidence in Pax5+/-Myd88+/- mice through an inflammation-dependent mechanism. Early induction of Myd88-independent Toll-like receptor 3 signaling results in a significant delay of leukemia development in Pax5+/- mice. Altogether, these findings identify a role for innate immunity dysregulation in leukemia, with important implications for understanding and therapeutic targeting of the preleukemic state in children.
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Affiliation(s)
- Marta Isidro-Hernández
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Ana Casado-García
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Ninad Oak
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Silvia Alemán-Arteaga
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Belén Ruiz-Corzo
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Jorge Martínez-Cano
- Immune system development and function Unit, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas -Universidad Autónoma de Madrid), Madrid, Spain
| | - Andrea Mayado
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Servicio de Citometría, Departamento de Medicina, Biomedical Research Networking Centre on Cancer CIBER-CIBERONC (CB16/12/00400), Institute of Health Carlos III, and Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Elena G Sánchez
- Department of Pediatric Hematology and Oncology, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain
| | - Oscar Blanco
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Departamento de Anatomía Patológica, Universidad de Salamanca, Salamanca, Spain
| | - Ma Luisa Gaspar
- Immunobiology Department, Carlos III Health Institute, 28220, Majadahonda (Madrid), Spain
| | - Alberto Orfao
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Servicio de Citometría, Departamento de Medicina, Biomedical Research Networking Centre on Cancer CIBER-CIBERONC (CB16/12/00400), Institute of Health Carlos III, and Instituto de Biología Molecular y Celular del Cáncer, CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Diego Alonso-López
- Bioinformatics Unit, Cancer Research Center (CSIC-USAL), Salamanca, Spain
| | - Javier De Las Rivas
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CSIC-USAL), Salamanca, Spain
| | - Susana Riesco
- Department of Pediatrics, Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, Salamanca, 37007, Spain
| | - Pablo Prieto-Matos
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Department of Pediatrics, Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, Salamanca, 37007, Spain
| | - África González-Murillo
- Department of Pediatric Hematology and Oncology, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain
| | - Francisco Javier García Criado
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Departamento de Cirugía, , Universidad de Salamanca, Salamanca, Spain
| | - María Begoña García Cenador
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Departamento de Cirugía, , Universidad de Salamanca, Salamanca, Spain
| | - Manuel Ramírez-Orellana
- Department of Pediatric Hematology and Oncology, Hospital Infantil Universitario Niño Jesús, Universidad Autónoma de Madrid, Madrid, Spain
| | - Belén de Andrés
- Immunobiology Department, Carlos III Health Institute, 28220, Majadahonda (Madrid), Spain
| | - Carolina Vicente-Dueñas
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.
- Department of Pediatrics, Hospital Universitario de Salamanca, Paseo de San Vicente, 58-182, Salamanca, 37007, Spain.
| | - César Cobaleda
- Immune system development and function Unit, Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas -Universidad Autónoma de Madrid), Madrid, Spain.
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Isidro Sánchez-García
- Experimental Therapeutics and Translational Oncology Program, Instituto de Biología Molecular y Celular del Cáncer, CSIC-USAL, Campus M. de Unamuno s/n, Salamanca, Spain.
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.
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28
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Xu Y, Xue D, Kyani A, Bankhead A, Roy J, Ljungman M, Neamati N. First-in-Class NADH/Ubiquinone Oxidoreductase Core Subunit S7 (NDUFS7) Antagonist for the Treatment of Pancreatic Cancer. ACS Pharmacol Transl Sci 2023; 6:1164-1181. [PMID: 37588763 PMCID: PMC10425995 DOI: 10.1021/acsptsci.3c00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Indexed: 08/18/2023]
Abstract
Pancreatic cancer cells adapt to nutrient-scarce metabolic conditions by increasing their oxidative phosphorylation reserve to survive. Here, we present a first-in-class small-molecule NDUFS7 antagonist that inhibits oxidative phosphorylation (OXPHOS) for the treatment of pancreatic cancer. The lead compound, DX2-201, suppresses the proliferation of a panel of cell lines, and a metabolically stable analogue, DX3-213B, shows significant efficacy in a syngeneic model of pancreatic cancer. Exome sequencing of six out of six clones resistant to DX2-201 revealed a pV91M mutation in NDUFS7, providing direct evidence of its drug-binding site. In combination studies, DX2-201 showed synergy with multiple metabolic modulators, select OXPHOS inhibitors, and PARP inhibitors. Importantly, a combination with 2-deoxyglucose overcomes drug resistance in vivo. This study demonstrates that an efficacious treatment for pancreatic cancer can be achieved through inhibition of OXPHOS and direct binding to NDUFS7, providing a novel therapeutic strategy for this hard-to-treat cancer.
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Affiliation(s)
- Yibin Xu
- Department
of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Rogel
Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ding Xue
- Department
of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Rogel
Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Armita Kyani
- Department
of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Rogel
Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Armand Bankhead
- Rogel
Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biostatistics and Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan 48109, United States
| | - Joyeeta Roy
- Department
of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Rogel
Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mats Ljungman
- Rogel
Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Environmental Health Sciences, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nouri Neamati
- Department
of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Rogel
Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
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29
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Jeon H, Ahn J, Na B, Hong S, Sael L, Kim S, Yoon S, Baek D. AIVariant: a deep learning-based somatic variant detector for highly contaminated tumor samples. Exp Mol Med 2023; 55:1734-1742. [PMID: 37524869 PMCID: PMC10474289 DOI: 10.1038/s12276-023-01049-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 08/02/2023] Open
Abstract
The detection of somatic DNA variants in tumor samples with low tumor purity or sequencing depth remains a daunting challenge despite numerous attempts to address this problem. In this study, we constructed a substantially extended set of actual positive variants originating from a wide range of tumor purities and sequencing depths, as well as actual negative variants derived from sequencer-specific sequencing errors. A deep learning model named AIVariant, trained on this extended dataset, outperforms previously reported methods when tested under various tumor purities and sequencing depths, especially low tumor purity and sequencing depth.
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Affiliation(s)
- Hyeonseong Jeon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- Genome4me Inc., Seoul, 08826, Republic of Korea
| | - Junhak Ahn
- Genome4me Inc., Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byunggook Na
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soona Hong
- AIGENDRUG Co., Ltd., Seoul, 08826, Republic of Korea
| | - Lee Sael
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, Republic of Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungroh Yoon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daehyun Baek
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea.
- Genome4me Inc., Seoul, 08826, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea.
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30
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Yang L, Wang J, Altreuter J, Jhaveri A, Wong CJ, Song L, Fu J, Taing L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qiu X, Long HW, Michor F, Liu Y, Liu XS. Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nat Protoc 2023; 18:2404-2414. [PMID: 37391666 DOI: 10.1038/s41596-023-00841-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/22/2023] [Indexed: 07/02/2023]
Abstract
RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique for molecular profiling and immune characterization of tumors. In the past decade, many computational tools have been developed to characterize tumor immunity from gene expression data. However, the analysis of large-scale RNA-seq data requires bioinformatics proficiency, large computational resources and cancer genomics and immunology knowledge. In this tutorial, we provide an overview of computational analysis of bulk RNA-seq data for immune characterization of tumors and introduce commonly used computational tools with relevance to cancer immunology and immunotherapy. These tools have diverse functions such as evaluation of expression signatures, estimation of immune infiltration, inference of the immune repertoire, prediction of immunotherapy response, neoantigen detection and microbiome quantification. We describe the RNA-seq IMmune Analysis (RIMA) pipeline integrating many of these tools to streamline RNA-seq analysis. We also developed a comprehensive and user-friendly guide in the form of a GitBook with text and video demos to assist users in analyzing bulk RNA-seq data for immune characterization at both individual sample and cohort levels by using RIMA.
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Affiliation(s)
- Lin Yang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Li Song
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- School of Life Science and Technology, Tongji University, Shanghai, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Avinash Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Gali Bai
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
- The Ludwig Center at Harvard, Boston, MA, USA
| | - Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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31
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Talwar JV, Laub D, Pagadala MS, Castro A, Lewis M, Luebeck GE, Gorman BR, Pan C, Dong FN, Markianos K, Teerlink CC, Lynch J, Hauger R, Pyarajan S, Tsao PS, Morris GP, Salem RM, Thompson WK, Curtius K, Zanetti M, Carter H. Autoimmune alleles at the major histocompatibility locus modify melanoma susceptibility. Am J Hum Genet 2023; 110:1138-1161. [PMID: 37339630 PMCID: PMC10357503 DOI: 10.1016/j.ajhg.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/22/2023] Open
Abstract
Autoimmunity and cancer represent two different aspects of immune dysfunction. Autoimmunity is characterized by breakdowns in immune self-tolerance, while impaired immune surveillance can allow for tumorigenesis. The class I major histocompatibility complex (MHC-I), which displays derivatives of the cellular peptidome for immune surveillance by CD8+ T cells, serves as a common genetic link between these conditions. As melanoma-specific CD8+ T cells have been shown to target melanocyte-specific peptide antigens more often than melanoma-specific antigens, we investigated whether vitiligo- and psoriasis-predisposing MHC-I alleles conferred a melanoma-protective effect. In individuals with cutaneous melanoma from both The Cancer Genome Atlas (n = 451) and an independent validation set (n = 586), MHC-I autoimmune-allele carrier status was significantly associated with a later age of melanoma diagnosis. Furthermore, MHC-I autoimmune-allele carriers were significantly associated with decreased risk of developing melanoma in the Million Veteran Program (OR = 0.962, p = 0.024). Existing melanoma polygenic risk scores (PRSs) did not predict autoimmune-allele carrier status, suggesting these alleles provide orthogonal risk-relevant information. Mechanisms of autoimmune protection were neither associated with improved melanoma-driver mutation association nor improved gene-level conserved antigen presentation relative to common alleles. However, autoimmune alleles showed higher affinity relative to common alleles for particular windows of melanocyte-conserved antigens and loss of heterozygosity of autoimmune alleles caused the greatest reduction in presentation for several conserved antigens across individuals with loss of HLA alleles. Overall, this study presents evidence that MHC-I autoimmune-risk alleles modulate melanoma risk unaccounted for by current PRSs.
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Affiliation(s)
- James V Talwar
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - David Laub
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Meghana S Pagadala
- Biomedical Science Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrea Castro
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - McKenna Lewis
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Georg E Luebeck
- Public Health Sciences Division, Herbold Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Cuiping Pan
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA
| | - Frederick N Dong
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Kyriacos Markianos
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02115, USA
| | - Craig C Teerlink
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Julie Lynch
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard Hauger
- VA San Diego Healthcare System, La Jolla, CA, USA; Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA; Center of Excellence for Stress and Mental Health (CESAMH), VA San Diego Healthcare System, San Diego, CA, USA
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Department of Medicine, Brigham Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Philip S Tsao
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA 92093, USA
| | - Wesley K Thompson
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK 74136, USA
| | - Kit Curtius
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; The Laboratory of Immunology, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, Division of Hematology and Oncology, University of California San Diego, La Jolla, CA 92093, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
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32
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Ji S, Zhu T, Sethia A, Wang W. Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547569. [PMID: 37461467 PMCID: PMC10350007 DOI: 10.1101/2023.07.04.547569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Accurate detection of somatic mutations in DNA sequencing data is a fundamental prerequisite for cancer research. Previous analytical challenge was overcome by consensus mutation calling from four to five popular callers. This, however, increases the already nontrivial computing time from individual callers. Here, we launch MuSE2.0, powered by multi-step parallelization and efficient memory allocation, to resolve the computing time bottleneck. MuSE2.0 speeds up 50 times than MuSE1.0 and 8-80 times than other popular callers. Our benchmark study suggests combining MuSE2.0 and the recently expedited Strelka2 can achieve high efficiency and accuracy in analyzing large cancer genomic datasets.
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Affiliation(s)
- Shuangxi Ji
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tong Zhu
- NVIDIA Corporation, Santa Clara, CA, USA
| | | | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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33
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Qiu MZ, Chen Q, Zheng DY, Zhao Q, Wu QN, Zhou ZW, Yang LQ, Luo QY, Sun YT, Lai MY, Yuan SS, Wang FH, Luo HY, Wang F, Li YH, Zhang HZ, Xu RH. Precise microdissection of gastric mixed adeno-neuroendocrine carcinoma dissects its genomic landscape and evolutionary clonal origins. Cell Rep 2023; 42:112576. [PMID: 37285266 DOI: 10.1016/j.celrep.2023.112576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/02/2023] [Accepted: 05/15/2023] [Indexed: 06/09/2023] Open
Abstract
Gastric mixed adenoneuroendocrine carcinoma (MANEC) is a clinically aggressive and heterogeneous tumor composed of adenocarcinoma (ACA) and neuroendocrine carcinoma (NEC). The genomic properties and evolutionary clonal origins of MANEC remain unclear. We conduct whole-exome and multiregional sequencing on 101 samples from 33 patients to elucidate their evolutionary paths. We identify four significantly mutated genes, TP53, RB1, APC, and CTNNB1. MANEC resembles chromosomal instability stomach adenocarcinoma in that whole-genome doubling in MANEC is predominant and occurs earlier than most copy-number losses. All tumors are of monoclonal origin, and NEC components show more aggressive genomic properties than their ACA counterparts. The phylogenetic trees show two tumor divergence patterns, including sequential and parallel divergence. Furthermore, ACA-to-NEC rather than NEC-to-ACA transition is confirmed by immunohistochemistry on 6 biomarkers in ACA- and NEC-dominant regions. These results provide insights into the clonal origin and tumor differentiation of MANEC.
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Affiliation(s)
- Miao-Zhen Qiu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Qingjian Chen
- Department of Basic Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China; State Key Laboratory of Systems Medicine for Cancer, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Dan-Yang Zheng
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China; Department of Clinical Oncology, LKS Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Qi Zhao
- Department of Basic Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Qi-Nian Wu
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Zhi-Wei Zhou
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Li-Qiong Yang
- Department of Basic Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Qiu-Yun Luo
- Department of Basic Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Yu-Ting Sun
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Ming-Yu Lai
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Sha-Sha Yuan
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Feng-Hua Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Hui-Yan Luo
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Feng Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Yu-Hong Li
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Hui-Zhong Zhang
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China
| | - Rui-Hua Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China.
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34
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Minami JK, Morrow D, Bayley NA, Fernandez EG, Salinas JJ, Tse C, Zhu H, Su B, Plawat R, Jones A, Sammarco A, Liau LM, Graeber TG, Williams KJ, Cloughesy TF, Dixon SJ, Bensinger SJ, Nathanson DA. CDKN2A deletion remodels lipid metabolism to prime glioblastoma for ferroptosis. Cancer Cell 2023; 41:1048-1060.e9. [PMID: 37236196 PMCID: PMC10330677 DOI: 10.1016/j.ccell.2023.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/27/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023]
Abstract
Malignant tumors exhibit heterogeneous metabolic reprogramming, hindering the identification of translatable vulnerabilities for metabolism-targeted therapy. How molecular alterations in tumors promote metabolic diversity and distinct targetable dependencies remains poorly defined. Here we create a resource consisting of lipidomic, transcriptomic, and genomic data from 156 molecularly diverse glioblastoma (GBM) tumors and derivative models. Through integrated analysis of the GBM lipidome with molecular datasets, we identify CDKN2A deletion remodels the GBM lipidome, notably redistributing oxidizable polyunsaturated fatty acids into distinct lipid compartments. Consequently, CDKN2A-deleted GBMs display higher lipid peroxidation, selectively priming tumors for ferroptosis. Together, this study presents a molecular and lipidomic resource of clinical and preclinical GBM specimens, which we leverage to detect a therapeutically exploitable link between a recurring molecular lesion and altered lipid metabolism in GBM.
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Affiliation(s)
- Jenna K Minami
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Danielle Morrow
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas A Bayley
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Elizabeth G Fernandez
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jennifer J Salinas
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher Tse
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Henan Zhu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Baolong Su
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rhea Plawat
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Anthony Jones
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alessandro Sammarco
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Linda M Liau
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Kevin J Williams
- UCLA Lipidomics Core, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy F Cloughesy
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Steven J Bensinger
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA Lipidomics Core, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
| | - David A Nathanson
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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35
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Yang X, Xu X, Breuss MW, Antaki D, Ball LL, Chung C, Shen J, Li C, George RD, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov LB, Sebat JL, Gleeson JG. Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nat Biotechnol 2023; 41:870-877. [PMID: 36593400 PMCID: PMC10314968 DOI: 10.1038/s41587-022-01559-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 10/10/2022] [Indexed: 01/04/2023]
Abstract
Mosaic variants (MVs) reflect mutagenic processes during embryonic development and environmental exposure, accumulate with aging and underlie diseases such as cancer and autism. The detection of noncancer MVs has been computationally challenging due to the sparse representation of nonclonally expanded MVs. Here we present DeepMosaic, combining an image-based visualization module for single nucleotide MVs and a convolutional neural network-based classification module for control-independent MV detection. DeepMosaic was trained on 180,000 simulated or experimentally assessed MVs, and was benchmarked on 619,740 simulated MVs and 530 independent biologically tested MVs from 16 genomes and 181 exomes. DeepMosaic achieved higher accuracy compared with existing methods on biological data, with a sensitivity of 0.78, specificity of 0.83 and positive predictive value of 0.96 on noncancer whole-genome sequencing data, as well as doubling the validation rate over previous best-practice methods on noncancer whole-exome sequencing data (0.43 versus 0.18). DeepMosaic represents an accurate MV classifier for noncancer samples that can be implemented as an alternative or complement to existing methods.
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Affiliation(s)
- Xiaoxu Yang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
| | - Xin Xu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Martin W Breuss
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Danny Antaki
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Changuk Chung
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jiawei Shen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Chen Li
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Renee D George
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yuhe Cheng
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Jonathan L Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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36
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O'Connell KA, Yosufzai ZB, Campbell RA, Lobb CJ, Engelken HT, Gorrell LM, Carlson TB, Catana JJ, Mikdadi D, Bonazzi VR, Klenk JA. Accelerating genomic workflows using NVIDIA Parabricks. BMC Bioinformatics 2023; 24:221. [PMID: 37259021 PMCID: PMC10230726 DOI: 10.1186/s12859-023-05292-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 04/15/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND As genome sequencing becomes better integrated into scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing these vast datasets. Although much work has been done to reduce compute times using various configurations of traditional CPU computing infrastructures, Graphics Processing Units (GPUs) offer opportunities to accelerate genomic workflows by orders of magnitude. Here we benchmark one GPU-accelerated software suite called NVIDIA Parabricks on Amazon Web Services (AWS), Google Cloud Platform (GCP), and an NVIDIA DGX cluster. We benchmarked six variant calling pipelines, including two germline callers (HaplotypeCaller and DeepVariant) and four somatic callers (Mutect2, Muse, LoFreq, SomaticSniper). RESULTS We achieved up to 65 × acceleration with germline variant callers, bringing HaplotypeCaller runtimes down from 36 h to 33 min on AWS, 35 min on GCP, and 24 min on the NVIDIA DGX. Somatic callers exhibited more variation between the number of GPUs and computing platforms. On cloud platforms, GPU-accelerated germline callers resulted in cost savings compared with CPU runs, whereas some somatic callers were more expensive than CPU runs because their GPU acceleration was not sufficient to overcome the increased GPU cost. CONCLUSIONS Germline variant callers scaled well with the number of GPUs across platforms, whereas somatic variant callers exhibited more variation in the number of GPUs with the fastest runtimes, suggesting that, at least with the version of Parabricks used here, these workflows are less GPU optimized and require benchmarking on the platform of choice before being deployed at production scales. Our study demonstrates that GPUs can be used to greatly accelerate genomic workflows, thus bringing closer to grasp urgent societal advances in the areas of biosurveillance and personalized medicine.
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Affiliation(s)
- Kyle A O'Connell
- Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA
| | | | - Ross A Campbell
- Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA
| | - Collin J Lobb
- Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA
| | - Haley T Engelken
- Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA
| | - Laura M Gorrell
- Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA
| | - Thad B Carlson
- Cloud Managed Services, Deloitte Consulting LLP, Detroit, MI, 48226, USA
| | - Josh J Catana
- Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA
| | - Dina Mikdadi
- Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA
| | - Vivien R Bonazzi
- Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
| | - Juergen A Klenk
- Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
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37
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Trevarton AJ, Chang JT, Symmans WF. Simple combination of multiple somatic variant callers to increase accuracy. Sci Rep 2023; 13:8463. [PMID: 37231022 DOI: 10.1038/s41598-023-34925-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Publications comparing variant caller algorithms present discordant results with contradictory rankings. Caller performances are inconsistent and wide ranging, and dependent upon input data, application, parameter settings, and evaluation metric. With no single variant caller emerging as a superior standard, combinations or ensembles of variant callers have appeared in the literature. In this study, a whole genome somatic reference standard was used to derive principles to guide strategies for combining variant calls. Then, manually annotated variants called from the whole exome sequencing of a tumor were used to corroborate these general principles. Finally, we examined the ability of these principles to reduce noise in targeted sequencing.
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Affiliation(s)
- Alexander J Trevarton
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, The University of Texas Health Sciences Center, Houston, USA
| | - W Fraser Symmans
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
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38
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Vaisband M, Schubert M, Gassner FJ, Geisberger R, Greil R, Zaborsky N, Hasenauer J. Validation of genetic variants from NGS data using deep convolutional neural networks. BMC Bioinformatics 2023; 24:158. [PMID: 37081386 PMCID: PMC10116675 DOI: 10.1186/s12859-023-05255-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023] Open
Abstract
Accurate somatic variant calling from next-generation sequencing data is one most important tasks in personalised cancer therapy. The sophistication of the available technologies is ever-increasing, yet, manual candidate refinement is still a necessary step in state-of-the-art processing pipelines. This limits reproducibility and introduces a bottleneck with respect to scalability. We demonstrate that the validation of genetic variants can be improved using a machine learning approach resting on a Convolutional Neural Network, trained using existing human annotation. In contrast to existing approaches, we introduce a way in which contextual data from sequencing tracks can be included into the automated assessment. A rigorous evaluation shows that the resulting model is robust and performs on par with trained researchers following published standard operating procedure.
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Affiliation(s)
- Marc Vaisband
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center; Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, Paracelsus Medical University, Salzburg, Austria.
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.
| | - Maria Schubert
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center; Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Franz Josef Gassner
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center; Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Roland Geisberger
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center; Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center; Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center; Salzburg Cancer Research Institute - Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR); Cancer Cluster Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Jan Hasenauer
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
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39
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McGee RB, Oak N, Harrison L, Xu K, Nuccio R, Blake AK, Mostafavi R, Lewis S, Taylor LM, Kubal M, Ouma A, Hines-Dowell SJ, Cheng C, Furtado LV, Nichols KE. Pathogenic Variants in Adult-Onset Cancer Predisposition Genes in Pediatric Cancer: Prevalence and Impact on Tumor Molecular Features and Clinical Management. Clin Cancer Res 2023; 29:1243-1251. [PMID: 36693186 PMCID: PMC10642481 DOI: 10.1158/1078-0432.ccr-22-2482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/09/2022] [Accepted: 01/23/2023] [Indexed: 01/25/2023]
Abstract
PURPOSE Clinical genomic sequencing of pediatric tumors is increasingly uncovering pathogenic variants in adult-onset cancer predisposition genes (aoCPG). Nevertheless, it remains poorly understood how often aoCPG variants are of germline origin and whether they influence tumor molecular profiles and/or clinical care. In this study, we examined the prevalence, spectrum, and impacts of aoCPG variants on tumor genomic features and patient management at our institution. EXPERIMENTAL DESIGN This is a retrospective study of 1,018 children with cancer who underwent clinical genomic sequencing of their tumors. Tumor genomic data were queried for pathogenic variants affecting 24 preselected aoCPGs. Available tumor whole-genome sequencing (WGS) data were evaluated for second hit mutations, loss of heterozygosity (LOH), DNA mutational signatures, and homologous recombination deficiency (HRD). Patients whose tumors harbored one or more pathogenic aoCPG variants underwent subsequent germline testing based on hereditary cancer evaluation and family or provider preference. RESULTS Thirty-three patients (3%) had tumors harboring pathogenic variants affecting one or more aoCPGs. Among 21 tumors with sufficient WGS sequencing data, six (29%) harbored a second hit or LOH affecting the remaining aoCPG allele with four of these six tumors (67%) also exhibiting a DNA mutational signature consistent with the altered aoCPG. Two additional tumors demonstrated HRD, of uncertain relation to the identified aoCPG variant. Twenty-one of 26 patients (81%) completing germline testing were positive for the aoCPG variant in the germline. All germline-positive patients were counseled regarding future cancer risks, surveillance, and risk-reducing measures. No patients had immediate cancer therapy changed due to aoCPG data. CONCLUSIONS AoCPG variants are rare in pediatric tumors; however, many originate in the germline. Almost one third of tumor aoCPG variants examined exhibited a second hit and/or conferred an abnormal DNA mutational profile suggesting a role in tumor formation. aoCPG information aids in cancer risk prediction but is not commonly used to alter the treatment of pediatric cancers.
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Affiliation(s)
- Rose B. McGee
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Ninad Oak
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Lynn Harrison
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Regina Nuccio
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Alise K. Blake
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Roya Mostafavi
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Sara Lewis
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Leslie M. Taylor
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Manish Kubal
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Annastasia Ouma
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | - Cheng Cheng
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Larissa V. Furtado
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
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40
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Cotto KC, Feng YY, Ramu A, Richters M, Freshour SL, Skidmore ZL, Xia H, McMichael JF, Kunisaki J, Campbell KM, Chen THP, Rozycki EB, Adkins D, Devarakonda S, Sankararaman S, Lin Y, Chapman WC, Maher CA, Arora V, Dunn GP, Uppaluri R, Govindan R, Griffith OL, Griffith M. Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer. Nat Commun 2023; 14:1589. [PMID: 36949070 PMCID: PMC10033906 DOI: 10.1038/s41467-023-37266-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools ( www.regtools.org ), a computationally efficient, free, and open-source software package designed to integrate somatic variants from genomic data with splice junctions from bulk or single cell transcriptomic data to identify variants that may cause aberrant splicing. We apply RegTools to over 9000 tumor samples with both tumor DNA and RNA sequence data. RegTools discovers 235,778 events where a splice-associated variant significantly increases the splicing of a particular junction, across 158,200 unique variants and 131,212 unique junctions. To characterize these somatic variants and their associated splice isoforms, we annotate them with the Variant Effect Predictor, SpliceAI, and Genotype-Tissue Expression junction counts and compare our results to other tools that integrate genomic and transcriptomic data. While many events are corroborated by the aforementioned tools, the flexibility of RegTools also allows us to identify splice-associated variants in known cancer drivers, such as TP53, CDKN2A, and B2M, and other genes.
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Affiliation(s)
- Kelsy C Cotto
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Yang-Yang Feng
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan Richters
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharon L Freshour
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Zachary L Skidmore
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Huiming Xia
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua F McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason Kunisaki
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Katie M Campbell
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy Hung-Po Chen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily B Rozycki
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Douglas Adkins
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Siddhartha Devarakonda
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sumithra Sankararaman
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - William C Chapman
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Maher
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Vivek Arora
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Gavin P Dunn
- Department of Neurosurgery, Mass General Hospital, Boston, MA, USA
- Center for Brain Tumor Immunology and Immunotherapy, Mass General Hospital, Boston, MA, USA
| | - Ravindra Uppaluri
- Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ramaswamy Govindan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Obi L Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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Cortes-Ciriano I, Steele CD, Piculell K, Al-Ibraheemi A, Eulo V, Bui MM, Chatzipli A, Dickson BC, Borcherding DC, Feber A, Galor A, Hart J, Jones KB, Jordan JT, Kim RH, Lindsay D, Miller C, Nishida Y, Proszek PZ, Serrano J, Sundby RT, Szymanski JJ, Ullrich NJ, Viskochil D, Wang X, Snuderl M, Park PJ, Flanagan AM, Hirbe AC, Pillay N, Miller DT. Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA. Cancer Discov 2023; 13:654-671. [PMID: 36598417 PMCID: PMC9983734 DOI: 10.1158/2159-8290.cd-22-0786] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023]
Abstract
Malignant peripheral nerve sheath tumor (MPNST), an aggressive soft-tissue sarcoma, occurs in people with neurofibromatosis type 1 (NF1) and sporadically. Whole-genome and multiregional exome sequencing, transcriptomic, and methylation profiling of 95 tumor samples revealed the order of genomic events in tumor evolution. Following biallelic inactivation of NF1, loss of CDKN2A or TP53 with or without inactivation of polycomb repressive complex 2 (PRC2) leads to extensive somatic copy-number aberrations (SCNA). Distinct pathways of tumor evolution are associated with inactivation of PRC2 genes and H3K27 trimethylation (H3K27me3) status. Tumors with H3K27me3 loss evolve through extensive chromosomal losses followed by whole-genome doubling and chromosome 8 amplification, and show lower levels of immune cell infiltration. Retention of H3K27me3 leads to extensive genomic instability, but an immune cell-rich phenotype. Specific SCNAs detected in both tumor samples and cell-free DNA (cfDNA) act as a surrogate for H3K27me3 loss and immune infiltration, and predict prognosis. SIGNIFICANCE MPNST is the most common cause of death and morbidity for individuals with NF1, a relatively common tumor predisposition syndrome. Our results suggest that somatic copy-number and methylation profiling of tumor or cfDNA could serve as a biomarker for early diagnosis and to stratify patients into prognostic and treatment-related subgroups. This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Christopher D. Steele
- Research Department of Pathology, University College London Cancer Institute, Bloomsbury, London, United Kingdom
| | - Katherine Piculell
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Alyaa Al-Ibraheemi
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Vanessa Eulo
- Division of Oncology, Department of Internal Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Marilyn M. Bui
- Department of Pathology, Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Aikaterini Chatzipli
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Brendan C. Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Dana C. Borcherding
- Division of Oncology, Departments of Internal Medicine and Pediatrics, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Andrew Feber
- Clinical Genomics Translational Research, Institute of Cancer Research, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Alon Galor
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jesse Hart
- Department of Pathology, Lifespan Laboratories, Rhode Island Hospital, Providence, Rhode Island
| | - Kevin B. Jones
- Departments of Orthopaedics and Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Justin T. Jordan
- Pappas Center for Neuro-oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Raymond H. Kim
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Sinai Health System, Toronto, Ontario, Canada
- Hospital for Sick Children, University of Toronto, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Daniel Lindsay
- Department of Histopathology, Royal National Orthopaedic Hospital, NHS Trust, Middlesex, United Kingdom
| | - Colin Miller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Yoshihiro Nishida
- Department of Rehabilitation Medicine, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Paula Z. Proszek
- Clinical Genomics Translational Research, Institute of Cancer Research, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jonathan Serrano
- Department of Pathology, New York University Langone Health, Perlmutter Cancer Center, New York City, New York
| | - R. Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jeffrey J. Szymanski
- Division of Cancer Biology, Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Nicole J. Ullrich
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - David Viskochil
- Division of Medical Genetics, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Xia Wang
- GeneHome, Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, Perlmutter Cancer Center, New York City, New York
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Adrienne M. Flanagan
- Research Department of Pathology, University College London Cancer Institute, Bloomsbury, London, United Kingdom
- Department of Histopathology, Royal National Orthopaedic Hospital, NHS Trust, Middlesex, United Kingdom
| | - Angela C. Hirbe
- Division of Oncology, Departments of Internal Medicine and Pediatrics, Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri
| | - Nischalan Pillay
- Research Department of Pathology, University College London Cancer Institute, Bloomsbury, London, United Kingdom
- Department of Histopathology, Royal National Orthopaedic Hospital, NHS Trust, Middlesex, United Kingdom
| | - David T. Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
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42
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Zhivagui M, Hoda A, Valenzuela N, Yeh YY, Dai J, He Y, Nandi SP, Otlu B, Van Houten B, Alexandrov LB. DNA damage and somatic mutations in mammalian cells after irradiation with a nail polish dryer. Nat Commun 2023; 14:276. [PMID: 36650165 PMCID: PMC9845303 DOI: 10.1038/s41467-023-35876-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Ultraviolet A light is commonly emitted by UV-nail polish dryers with recent reports suggesting that long-term use may increase the risk for developing skin cancer. However, no experimental evaluation has been conducted to reveal the effect of radiation emitted by UV-nail polish dryers on mammalian cells. Here, we show that irradiation by a UV-nail polish dryer causes high levels of reactive oxygen species, consistent with 8-oxo-7,8-dihydroguanine damage and mitochondrial dysfunction. Analysis of somatic mutations reveals a dose-dependent increase of C:G>A:T substitutions in irradiated samples with mutagenic patterns similar to mutational signatures previously attributed to reactive oxygen species. In summary, this study demonstrates that radiation emitted by UV-nail polish dryers can both damage DNA and permanently engrave mutations on the genomes of primary mouse embryonic fibroblasts, human foreskin fibroblasts, and human epidermal keratinocytes.
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Affiliation(s)
- Maria Zhivagui
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Areebah Hoda
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
| | | | - Yi-Yu Yeh
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
| | - Jason Dai
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Shuvro P Nandi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Burcak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA.,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
| | - Bennett Van Houten
- UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA. .,Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA. .,Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA.
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43
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Scotto di Carlo F, Russo S, Muyas F, Mangini M, Garribba L, Pazzaglia L, Genesio R, Biamonte F, De Luca AC, Santaguida S, Scotlandi K, Cortés-Ciriano I, Gianfrancesco F. Profilin 1 deficiency drives mitotic defects and reduces genome stability. Commun Biol 2023; 6:9. [PMID: 36599901 PMCID: PMC9813376 DOI: 10.1038/s42003-022-04392-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Profilin 1-encoded by PFN1-is a small actin-binding protein with a tumour suppressive role in various adenocarcinomas and pagetic osteosarcomas. However, its contribution to tumour development is not fully understood. Using fix and live cell imaging, we report that Profilin 1 inactivation results in multiple mitotic defects, manifested prominently by anaphase bridges, multipolar spindles, misaligned and lagging chromosomes, and cytokinesis failures. Accordingly, next-generation sequencing technologies highlighted that Profilin 1 knock-out cells display extensive copy-number alterations, which are associated with complex genome rearrangements and chromothripsis events in primary pagetic osteosarcomas with Profilin 1 inactivation. Mechanistically, we show that Profilin 1 is recruited to the spindle midzone at anaphase, and its deficiency reduces the supply of actin filaments to the cleavage furrow during cytokinesis. The mitotic defects are also observed in mouse embryonic fibroblasts and mesenchymal cells deriving from a newly generated knock-in mouse model harbouring a Pfn1 loss-of-function mutation. Furthermore, nuclear atypia is also detected in histological sections of mutant femurs. Thus, our results indicate that Profilin 1 has a role in regulating cell division, and its inactivation triggers mitotic defects, one of the major mechanisms through which tumour cells acquire chromosomal instability.
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Affiliation(s)
- Federica Scotto di Carlo
- grid.5326.20000 0001 1940 4177Institute of Genetics and Biophysics “Adriano Buzzati-Traverso” (IGB), National Research Council of Italy (CNR), Naples, Italy
| | - Sharon Russo
- grid.5326.20000 0001 1940 4177Institute of Genetics and Biophysics “Adriano Buzzati-Traverso” (IGB), National Research Council of Italy (CNR), Naples, Italy ,grid.9841.40000 0001 2200 8888Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Francesc Muyas
- grid.52788.300000 0004 0427 7672European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Maria Mangini
- grid.429047.c0000 0004 6477 0469Institute for Experimental Endocrinology and Oncology, “G. Salvatore” (IEOS), National Research Council of Italy (CNR), Naples, Italy
| | - Lorenza Garribba
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Laura Pazzaglia
- grid.419038.70000 0001 2154 6641IRCCS Istituto Ortopedico Rizzoli, Laboratory of Experimental Oncology, Bologna, Italy
| | - Rita Genesio
- grid.4691.a0000 0001 0790 385XDepartment of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Flavia Biamonte
- grid.411489.10000 0001 2168 2547Department of Experimental and Clinical Medicine, Magna Graecia University, Catanzaro, Italy ,grid.411489.10000 0001 2168 2547Center of Interdepartmental Services (CIS), Magna Graecia University, Catanzaro, Italy
| | - Anna Chiara De Luca
- grid.429047.c0000 0004 6477 0469Institute for Experimental Endocrinology and Oncology, “G. Salvatore” (IEOS), National Research Council of Italy (CNR), Naples, Italy
| | - Stefano Santaguida
- grid.15667.330000 0004 1757 0843Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Katia Scotlandi
- grid.419038.70000 0001 2154 6641IRCCS Istituto Ortopedico Rizzoli, Laboratory of Experimental Oncology, Bologna, Italy
| | - Isidro Cortés-Ciriano
- grid.52788.300000 0004 0427 7672European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fernando Gianfrancesco
- grid.5326.20000 0001 1940 4177Institute of Genetics and Biophysics “Adriano Buzzati-Traverso” (IGB), National Research Council of Italy (CNR), Naples, Italy
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44
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Seillier L, Peifer M. Reconstructing Phylogenetic Relationship in Bladder Cancer: A Methodological Overview. Methods Mol Biol 2023; 2684:113-132. [PMID: 37410230 DOI: 10.1007/978-1-0716-3291-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Bladder cancer (BC) expresses itself as a highly heterogeneous disease both at the histological and molecular level, often occurring as synchronous or metachronous multifocal disease with high risk of recurrence and potential to metastasize. Multiple sequencing studies focusing on both non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC) gave insights into the extent of both inter- and intrapatient heterogeneity, but many questions on clonal evolution in BC remain unanswered. In this review article, we provide an overview over the technical and theoretical concepts linked to reconstructing evolutionary trajectories in BC and propose a set of tools and established software for phylogenetic analysis.
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Affiliation(s)
| | - Martin Peifer
- Department of Translational Genomics, University of Cologne, Cologne, Germany
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45
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Li Z, Cong Y, Chen X, Qi J, Sun J, Yan T, Yang H, Liu J, Lu E, Wang L, Li J, Hu H, Zhang C, Yang Q, Yao J, Yao P, Jiang Q, Liu W, Song J, Carin L, Chen Y, Zhao S, Gao X. Vision transformer-based weakly supervised histopathological image analysis of primary brain tumors. iScience 2022; 26:105872. [PMID: 36647383 PMCID: PMC9839963 DOI: 10.1016/j.isci.2022.105872] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/03/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
Diagnosis of primary brain tumors relies heavily on histopathology. Although various computational pathology methods have been developed for automated diagnosis of primary brain tumors, they usually require neuropathologists' annotation of region of interests or selection of image patches on whole-slide images (WSI). We developed an end-to-end Vision Transformer (ViT) - based deep learning architecture for brain tumor WSI analysis, yielding a highly interpretable deep-learning model, ViT-WSI. Based on the principle of weakly supervised machine learning, ViT-WSI accomplishes the task of major primary brain tumor type and subtype classification. Using a systematic gradient-based attribution analysis procedure, ViT-WSI can discover diagnostic histopathological features for primary brain tumors. Furthermore, we demonstrated that ViT-WSI has high predictive power of inferring the status of three diagnostic glioma molecular markers, IDH1 mutation, p53 mutation, and MGMT methylation, directly from H&E-stained histopathological images, with patient level AUC scores of 0.960, 0.874, and 0.845, respectively.
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Affiliation(s)
- Zhongxiao Li
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Yuwei Cong
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin 150001, People’s Republic of China
| | - Xin Chen
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Jiping Qi
- Department of Pathology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin 150001, People’s Republic of China,Corresponding author
| | - Jingxian Sun
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Tao Yan
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - He Yang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Junsi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Enzhou Lu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Lixiang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Jiafeng Li
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Hong Hu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | | | - Quan Yang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Jiawei Yao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Penglei Yao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Qiuyi Jiang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Wenwu Liu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia,Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Lawrence Carin
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,Corresponding author
| | - Yupeng Chen
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, PR China,Corresponding author
| | - Shiguang Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province 150001, China,Department of Neurosurgery, Shenzhen University General Hospital, Shenzhen, Guangdong Province 518100, China,Corresponding author
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,Corresponding author
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46
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Castro-Mondragon JA, Aure M, Lingjærde O, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen V, Mathelier A. Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers. Nucleic Acids Res 2022; 50:12131-12148. [PMID: 36477895 PMCID: PMC9757053 DOI: 10.1093/nar/gkac1143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/03/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Most cancer alterations occur in the noncoding portion of the human genome, where regulatory regions control gene expression. The discovery of noncoding mutations altering the cells' regulatory programs has been limited to few examples with high recurrence or high functional impact. Here, we show that transcription factor binding sites (TFBSs) have similar mutation loads to those in protein-coding exons. By combining cancer somatic mutations in TFBSs and expression data for protein-coding and miRNA genes, we evaluate the combined effects of transcriptional and post-transcriptional alterations on the regulatory programs in cancers. The analysis of seven TCGA cohorts culminates with the identification of protein-coding and miRNA genes linked to mutations at TFBSs that are associated with a cascading trans-effect deregulation on the cells' regulatory programs. Our analyses of cis-regulatory mutations associated with miRNAs recurrently predict 12 mature miRNAs (derived from 7 precursors) associated with the deregulation of their target gene networks. The predictions are enriched for cancer-associated protein-coding and miRNA genes and highlight cis-regulatory mutations associated with the dysregulation of key pathways associated with carcinogenesis. By combining transcriptional and post-transcriptional regulation of gene expression, our method predicts cis-regulatory mutations related to the dysregulation of key gene regulatory networks in cancer patients.
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Affiliation(s)
- Jaime A Castro-Mondragon
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Miriam Ragle Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Gaustadalléen 23 B, N-0373 Oslo, Norway
- KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Ullernchausseen 70, N-0372 Oslo, Norway
| | - Anita Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - John W M Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway
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47
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The Somatic Mutation Landscape of UDP-Glycosyltransferase ( UGT) Genes in Human Cancers. Cancers (Basel) 2022; 14:cancers14225708. [PMID: 36428799 PMCID: PMC9688768 DOI: 10.3390/cancers14225708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The human UDP-glycosyltransferase (UGTs) superfamily has a critical role in the metabolism of anticancer drugs and numerous pro/anti-cancer molecules (e.g., steroids, lipids, fatty acids, bile acids and carcinogens). Recent studies have shown wide and abundant expression of UGT genes in human cancers. However, the extent to which UGT genes acquire somatic mutations within tumors remains to be systematically investigated. In the present study, our comprehensive analysis of the somatic mutation profiles of 10,069 tumors from 33 different TCGA cancer types identified 3427 somatic mutations in UGT genes. Overall, nearly 18% (1802/10,069) of the assessed tumors had mutations in UGT genes with huge variations in mutation frequency across different cancer types, ranging from over 25% in five cancers (COAD, LUAD, LUSC, SKCM and UCSC) to less than 5% in eight cancers (LAML, MESO, PCPG, PAAD, PRAD, TGCT, THYM and UVM). All 22 UGT genes showed somatic mutations in tumors, with UGT2B4, UGT3A1 and UGT3A2 showing the largest number of mutations (289, 307 and 255 mutations, respectively). Nearly 65% (2260/3427) of the mutations were missense, frame-shift and nonsense mutations that have been predicted to code for variant UGT proteins. Furthermore, about 10% (362/3427) of the mutations occurred in non-coding regions (5' UTR, 3' UTR and splice sites) that may be able to alter the efficiency of translation initiation, miRNA regulation or the splicing of UGT transcripts. In conclusion, our data show widespread somatic mutations of UGT genes in human cancers that may affect the capacity of cancer cells to metabolize anticancer drugs and endobiotics that control pro/anti-cancer signaling pathways. This highlights their potential utility as biomarkers for predicting therapeutic efficacy and clinical outcomes.
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Redman JM, Friedman J, Robbins Y, Sievers C, Yang X, Lassoued W, Sinkoe A, Papanicolau-Sengos A, Lee CC, Marte JL, Turkbey E, Mydlarz W, Joshi A, London NR, Pierce M, Taylor R, Hong S, Nguyen A, Soon-Shiong P, Schlom J, Gulley JL, Allen CT. Enhanced neoepitope-specific immunity following neoadjuvant PD-L1 and TGF-β blockade in HPV-unrelated head and neck cancer. J Clin Invest 2022; 132:e161400. [PMID: 35727629 PMCID: PMC9479764 DOI: 10.1172/jci161400] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUNDHead and neck squamous cell carcinoma not associated with HPV (HPV-unrelated HNSCC) is associated with a high rate of recurrence and poor survival.METHODSWe conducted a clinical trial in 14 patients with newly diagnosed HPV-unrelated HNSCC to evaluate the safety and efficacy of neoadjuvant bintrafusp alfa, a bifunctional fusion protein that blocks programmed death ligand 1 (PD-L1) and neutralizes TGF-β.RESULTSBintrafusp alfa was well tolerated, and no treatment-associated surgical delays or complications occurred. Objective pathologic responses (PRs) were observed, and 12 of the 14 (86%) patients were alive and disease free at 1 year. Alterations in Treg infiltration and spatial distribution relative to proliferating CD8+ T cells indicated a reversal of Treg immunosuppression in the primary tumor. Detection of neoepitope-specific tumor T cell responses, but not virus-specific responses, correlated with the development of a PR. Detection of neoepitope-specific responses and PRs in tumors was not correlated with genomic features or tumor antigenicity but was associated with reduced pretreatment myeloid cell tumor infiltration. These results indicate that dual PD-L1 and TGF-β blockade can safely enhance tumor antigen-specific immunity and highlight the feasibility of multimechanism neoadjuvant immunotherapy for patients with HPV-unrelated HNSCC.CONCLUSIONOur studies provide insight into the ability of neoadjuvant immunotherapy to induce polyclonal neoadjuvant-specific T cell responses in tumors and suggest that features of the tumor microenvironment, such as myeloid cell infiltration, may be a major determinant of enhanced antitumor immunity following such treatment.TRIAL REGISTRATIONClinicalTrials.gov NCT04247282.FUNDINGThis work was funded by the Center for Cancer Research, the NCI, and the Intramural Research Program of the NIDCD, NIH. Bintrafusp alfa was provided by the health care business of Merck KGaA (Darmstadt, Germany), through a Cooperative Research and Development Agreement with the NCI. Additional funding was provided by ImmunityBio through a Cooperative Research and Development Agreement with the NIDCD.
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Affiliation(s)
- Jason M. Redman
- Genitourinary Malignancy Branch and
- Laboratory of Tumor Immunology and Biology, National Cancer Institute (NCI), Center for Cancer Research, NIH, Bethesda, Maryland, USA
| | - Jay Friedman
- Section on Translational Tumor Immunology, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Yvette Robbins
- Section on Translational Tumor Immunology, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Cem Sievers
- Section on Translational Tumor Immunology, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Xinping Yang
- Section on Translational Tumor Immunology, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
| | - Wiem Lassoued
- Tumor Immune Microenvironment Laboratory, Genitourinary Malignancy Branch, NCI, and
| | | | | | - Chyi-Chia Lee
- Laboratory of Pathology, Center for Cancer Research, NIH, Bethesda, Maryland, USA
| | | | - Evrim Turkbey
- Radiology and Imaging Sciences, NIH Clinical Center, Bethesda, Maryland, USA
| | - Wojtek Mydlarz
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Arjun Joshi
- Division of Otolaryngology–Head and Neck Surgery, Department of Surgery, George Washington University, Washington, DC, USA
| | - Nyall R. London
- Department of Otolaryngology–Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Matthew Pierce
- Department of Otolaryngology–Head and Neck Surgery, Georgetown University School of Medicine, Washington, DC, USA
| | - Rodney Taylor
- Department of Otolaryngology–Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Steven Hong
- Department of Otolaryngology–Head and Neck Surgery, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | | | | | - Jeffrey Schlom
- Laboratory of Tumor Immunology and Biology, National Cancer Institute (NCI), Center for Cancer Research, NIH, Bethesda, Maryland, USA
| | | | - Clint T. Allen
- Section on Translational Tumor Immunology, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland, USA
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49
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Song H, Liu Y, Tan Y, Zhang Y, Jin W, Chen L, Wu S, Yan J, Li J, Chen Z, Chen S, Wang K. Recurrent noncoding somatic and germline WT1 variants converge to disrupt MYB binding in acute promyelocytic leukemia. Blood 2022; 140:1132-1144. [PMID: 35653587 PMCID: PMC9461475 DOI: 10.1182/blood.2021014945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Genetic alternations can occur at noncoding regions, but how they contribute to cancer pathogenesis is poorly understood. Here, we established a mutational landscape of cis-regulatory regions (CREs) in acute promyelocytic leukemia (APL) based on whole-genome sequencing analysis of paired tumor and germline samples from 24 patients and epigenetic profiling of 16 patients. Mutations occurring in CREs occur preferentially in active enhancers bound by the complex of master transcription factors in APL. Among significantly enriched mutated CREs, we found a recurrently mutated region located within the third intron of WT1, an essential regulator of normal and malignant hematopoiesis. Focusing on noncoding mutations within this WT1 intron, an analysis on 169 APL patients revealed that somatic mutations were clustered into a focal hotspot region, including one site identified as a germline polymorphism contributing to APL risk. Significantly decreased WT1 expression was observed in APL patients bearing somatic and/or germline noncoding WT1 variants. Furthermore, biallelic WT1 inactivation was recurrently found in APL patients with noncoding WT1 variants, which resulted in the complete loss of WT1. The high incidence of biallelic inactivation suggested the tumor suppressor activity of WT1 in APL. Mechanistically, noncoding WT1 variants disrupted MYB binding on chromatin and suppressed the enhancer activity and WT1 expression through destroying the chromatin looping formation. Our study highlights the important role of noncoding variants in the leukemogenesis of APL.
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Affiliation(s)
- Huan Song
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yabin Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen Jin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shishuang Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinsong Yan
- Department of Hematology, the Second Hospital of Dalian Medical University, Dalian, China
| | - Junmin Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; and
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50
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Hu J, Jarusiewicz J, Du G, Nishiguchi G, Yoshimura S, Panetta JC, Li Z, Min J, Yang L, Chepyala D, Actis M, Reyes N, Smart B, Pui CH, Teachey DT, Rankovic Z, Yang JJ. Preclinical evaluation of proteolytic targeting of LCK as a therapeutic approach in T cell acute lymphoblastic leukemia. Sci Transl Med 2022; 14:eabo5228. [PMID: 36001679 PMCID: PMC9730446 DOI: 10.1126/scitranslmed.abo5228] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy, and there is an unmet need for targeted therapies, especially for patients with relapsed disease. We have recently identified pre-T cell receptor and lymphocyte-specific protein tyrosine kinase (LCK) signaling as a common therapeutic vulnerability in T-ALL. LCK inhibitor dasatinib showed efficacy against T-ALL in preclinical studies and in patients with T-ALL; however, this is transient in most cases. Leveraging the proteolysis targeting chimera (PROTAC) approach, we developed a series of LCK degraders using dasatinib as an LCK ligand and phenyl-glutarimide as a cereblon-directing moiety. Our lead compound SJ11646 exhibited marked efficiency in cereblon-mediated LCK degradation in T-ALL cells. Relative to dasatinib, SJ11646 showed up to three orders of magnitude higher cytotoxicity in LCK-activated T-ALL cell lines and primary leukemia samples in vitro, with drastically prolonged suppression of LCK signaling. In vivo pharmacokinetic and pharmacodynamic profiling indicated a 630% increase in the duration of LCK suppression by SJ11646 over dasatinib in patient-derived xenograft models of T-ALL, which translated into its extended leukemia-free survival over dasatinib in vivo. Last, SJ11646 retained a high binding affinity to 51 human kinases, particularly ABL1, KIT, and DDR1, all of which are known drug targets in other cancers. Together, our dasatinib-based phenyl-glutarimide PROTACs are promising therapeutic agents in T-ALL and valuable tools for developing degradation-based therapeutics for other cancers.
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Affiliation(s)
- Jianzhong Hu
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Jamie Jarusiewicz
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Guoqing Du
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Gisele Nishiguchi
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Satoshi Yoshimura
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - John C. Panetta
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Zhenhua Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Jaeki Min
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Lei Yang
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Divyabharathi Chepyala
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Marisa Actis
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA
| | - Noemi Reyes
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Brandon Smart
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - David T. Teachey
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Zoran Rankovic
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital; Memphis, TN, 38105, USA,,Correspondence to: Jun J. Yang Ph.D., Member, Department of Pharmacy and Pharmaceutical Sciences, Department of Oncology, ; Zoran Rankovic Ph.D., Director, CBT Chemistry Centers, Department of Chemical Biology & Therapeutics, ; St. Jude Children’s Research Hospital, 262 Danny Thomas Pl., Memphis, TN 38105
| | - Jun J. Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA,,Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA,,Correspondence to: Jun J. Yang Ph.D., Member, Department of Pharmacy and Pharmaceutical Sciences, Department of Oncology, ; Zoran Rankovic Ph.D., Director, CBT Chemistry Centers, Department of Chemical Biology & Therapeutics, ; St. Jude Children’s Research Hospital, 262 Danny Thomas Pl., Memphis, TN 38105
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